ENCFF992QZV bed narrowPeak optimal idr thresholded peaks ENCSR494TDU ChIP-seq EFO:0002067 K562 cell line Homo sapiens NRF1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF312EZM, ENCFF477OCU, ENCFF940NRT 622007 ENCODE Processing Pipeline abd4e1b435d690187f35c0bf71fe5cdb https://www.encodeproject.org/files/ENCFF992QZV/@@download/ENCFF992QZV.bed.gz hg19 released mild to moderate bottlenecking ENCFF494ZUY bed narrowPeak optimal idr thresholded peaks ENCSR654CQU ChIP-seq EFO:0002067 K562 cell line Homo sapiens SNIP1-human DNA False 2017-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF039BZL, ENCFF363FXM, ENCFF842STK 52646 ENCODE Processing Pipeline d84d3f827e6208c9292af63c7bd62158 https://www.encodeproject.org/files/ENCFF494ZUY/@@download/ENCFF494ZUY.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF965ZRH bed narrowPeak optimal idr thresholded peaks ENCSR348JOJ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MTA1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF007YBE, ENCFF078PIE, ENCFF232YBQ 230360 ENCODE Processing Pipeline 034fb3e1a66d522847d0967705c3236c https://www.encodeproject.org/files/ENCFF965ZRH/@@download/ENCFF965ZRH.bed.gz hg19 released antibody characterized with exemption ENCFF545DAF bed narrowPeak optimal idr thresholded peaks ENCSR117WTM ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ZNF24-human DNA False 2016-03-02 ENCODE 1, 2 ENCFF001TDO, ENCFF670KBE, ENCFF694BDZ, ENCFF710KBI 243151 ENCODE Processing Pipeline 2d74e845180c2708a1b8a2f4ba901591 https://www.encodeproject.org/files/ENCFF545DAF/@@download/ENCFF545DAF.bed.gz hg19 released low read depth, missing genetic modification characterization ENCFF493TZM bed narrowPeak optimal idr thresholded peaks ENCSR744WOO ChIP-seq EFO:0002067 K562 cell line Homo sapiens TCF12-human DNA False 2016-10-24 ENCODE 1, 2 ENCFF001TDO, ENCFF334SEU, ENCFF337ISL, ENCFF870JMX 509065 ENCODE Processing Pipeline 3683eb367b6ea3aaab2799d3a4abd218 https://www.encodeproject.org/files/ENCFF493TZM/@@download/ENCFF493TZM.bed.gz hg19 released antibody characterized with exemption ENCFF717TWA bed narrowPeak optimal idr thresholded peaks ENCSR550HCT ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-KLF1-human DNA False 2016-01-14 ENCODE 1, 2 ENCFF001TDO, ENCFF255LGM, ENCFF830SMA, ENCFF842XXA 221756 ENCODE Processing Pipeline d6e556ebcba694582483815e5740993f https://www.encodeproject.org/files/ENCFF717TWA/@@download/ENCFF717TWA.bed.gz hg19 released missing genetic modification characterization missing mapped reads lengths ENCFF157UUF bed narrowPeak optimal idr thresholded peaks ENCSR657EOF ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFRKB-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF235FNK, ENCFF338NAH, ENCFF674FOQ 360420 ENCODE Processing Pipeline f149fb690dd6079819477e00024ce227 https://www.encodeproject.org/files/ENCFF157UUF/@@download/ENCFF157UUF.bed.gz hg19 released low read depth ENCFF273BVT bed narrowPeak optimal idr thresholded peaks ENCSR117KWH ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF207-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF432JWQ, ENCFF744DJH, ENCFF790EAG 253776 ENCODE Processing Pipeline 723ae98f692a0545c08fab0660c49ebe https://www.encodeproject.org/files/ENCFF273BVT/@@download/ENCFF273BVT.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF106DAY bed narrowPeak optimal idr thresholded peaks ENCSR720HUL ChIP-seq EFO:0002067 K562 cell line Homo sapiens E2F1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF199PBO, ENCFF260KBY, ENCFF721GUV 431592 ENCODE Processing Pipeline eebcfeb474d20d087492413655d9c57c https://www.encodeproject.org/files/ENCFF106DAY/@@download/ENCFF106DAY.bed.gz hg19 released mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity experiment not submitted to GEO poor library complexity, severe bottlenecking, partially characterized antibody ENCFF455YHJ bed narrowPeak optimal idr thresholded peaks ENCSR192AFN ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens PAX8-human DNA False 2017-11-30 ENCODE 1, 2 ENCFF001TDO, ENCFF268ECX, ENCFF350LWS, ENCFF769CZK 73718 ENCODE Processing Pipeline 2598e2b4d1582b2d4fd97e93d48f9d08 https://www.encodeproject.org/files/ENCFF455YHJ/@@download/ENCFF455YHJ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity experiment not submitted to GEO ENCFF282SXB bed narrowPeak optimal idr thresholded peaks ENCSR949IWY ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens PAX8-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF014SMM, ENCFF291LKR, ENCFF371FPA 52089 ENCODE Processing Pipeline 35d8b5977ee67e6d987d5b8a11f091b9 https://www.encodeproject.org/files/ENCFF282SXB/@@download/ENCFF282SXB.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF410EDG bed narrowPeak optimal idr thresholded peaks ENCSR113LAS ChIP-seq EFO:0002067 K562 cell line Homo sapiens MTA2-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF094YIY, ENCFF186VAU, ENCFF501DZY 259215 ENCODE Processing Pipeline dcb6e6f91e09c643f12408b087773474 https://www.encodeproject.org/files/ENCFF410EDG/@@download/ENCFF410EDG.bed.gz hg19 released low read depth ENCFF408FQC bed narrowPeak optimal idr thresholded peaks ENCSR876GXA ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZBTB33-human DNA False 2016-06-23 ENCODE 3, 4 ENCFF001TDO, ENCFF108BVL, ENCFF388RWJ, ENCFF778NFD 974557 ENCODE Processing Pipeline a9f515a615c9736874c5b02b3ef2f106 https://www.encodeproject.org/files/ENCFF408FQC/@@download/ENCFF408FQC.bed.gz hg19 released low read depth ENCFF958KNK bed narrowPeak optimal idr thresholded peaks ENCSR028UIU ChIP-seq EFO:0002067 K562 cell line Homo sapiens ATF3-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF034DTN, ENCFF164BVB, ENCFF263MQY 1074003 ENCODE Processing Pipeline 9766f5508a9d7c4285265a20084a2850 https://www.encodeproject.org/files/ENCFF958KNK/@@download/ENCFF958KNK.bed.gz hg19 released mild to moderate bottlenecking, inconsistent platforms, moderate library complexity experiment not submitted to GEO ENCFF249EZR bed narrowPeak optimal idr thresholded peaks ENCSR863KUB ChIP-seq EFO:0002067 K562 cell line Homo sapiens TCF7-human DNA False 2016-01-14 ENCODE 1, 2 ENCFF001TDO, ENCFF086FEW, ENCFF127VYL, ENCFF588ZYR 107201 ENCODE Processing Pipeline e6d734cd2dddbdb65175f4aac5d619c6 https://www.encodeproject.org/files/ENCFF249EZR/@@download/ENCFF249EZR.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption missing control alignments ENCFF909FRA bed narrowPeak optimal idr thresholded peaks ENCSR041XML ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SRF-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF172UOB, ENCFF467WTS, ENCFF500GHH 355186 ENCODE Processing Pipeline 61fffb75b6f30e6189a0319942b70dab https://www.encodeproject.org/files/ENCFF909FRA/@@download/ENCFF909FRA.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity experiment not submitted to GEO partially characterized antibody ENCFF370ENX bed narrowPeak optimal idr thresholded peaks ENCSR796ITY ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFIC-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF292SNP, ENCFF351DKB, ENCFF754CMK 878417 ENCODE Processing Pipeline c5c8948cb0e3434da4fa620f09ef9812 https://www.encodeproject.org/files/ENCFF370ENX/@@download/ENCFF370ENX.bed.gz hg19 released mild to moderate bottlenecking, inconsistent platforms ENCFF925DJG bed narrowPeak optimal idr thresholded peaks ENCSR953DVM ChIP-seq EFO:0002067 K562 cell line Homo sapiens E2F8-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF133EYO, ENCFF696BJA, ENCFF904YUH 199330 ENCODE Processing Pipeline a54bfc70ca37fae47890b441013320dd https://www.encodeproject.org/files/ENCFF925DJG/@@download/ENCFF925DJG.bed.gz hg19 released mild to moderate bottlenecking, low read depth experiment not submitted to GEO partially characterized antibody ENCFF526EEI bed narrowPeak optimal idr thresholded peaks ENCSR975SSR ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ELF1-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF074NKQ, ENCFF241QBV, ENCFF769RKU 313782 ENCODE Processing Pipeline 1f4cf632566898df354da40c0e111751 https://www.encodeproject.org/files/ENCFF526EEI/@@download/ENCFF526EEI.bed.gz hg19 released missing genetic modification characterization ENCFF886VSU bed narrowPeak optimal idr thresholded peaks ENCSR948VFL ChIP-seq EFO:0002067 K562 cell line Homo sapiens IKZF1-human DNA False 2016-10-11 ENCODE 1, 2 ENCFF001TDO, ENCFF165OLG, ENCFF320JKZ, ENCFF519QZC 870116 ENCODE Processing Pipeline 75a920f51d6077f2f65ffc7fadadfe2e https://www.encodeproject.org/files/ENCFF886VSU/@@download/ENCFF886VSU.bed.gz hg19 released ENCFF566WSG bed narrowPeak optimal idr thresholded peaks ENCSR382MOM ChIP-seq UBERON:0002107 liver tissue Homo sapiens YY1-human DNA False 2016-03-31 ENCODE 1, 2 ENCFF001TDO, ENCFF079CJA, ENCFF086YFF, ENCFF884TKH 1009004 ENCODE Processing Pipeline 1bd5d50abbe1d858675db04c9d86fd4a https://www.encodeproject.org/files/ENCFF566WSG/@@download/ENCFF566WSG.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF144PPR bed narrowPeak optimal idr thresholded peaks ENCSR837EYC ChIP-seq EFO:0002067 K562 cell line Homo sapiens NRF1-human DNA False 2016-06-16 ENCODE 1, 2 ENCFF001TDO, ENCFF559ITE, ENCFF606MZK, ENCFF892HJT 370811 ENCODE Processing Pipeline ed341ef382b1729a4467c26b9d7afc00 https://www.encodeproject.org/files/ENCFF144PPR/@@download/ENCFF144PPR.bed.gz hg19 released low read depth, moderate library complexity ENCFF266KLW bed narrowPeak optimal idr thresholded peaks ENCSR338MMB ChIP-seq UBERON:0002107 liver tissue Homo sapiens NR2F2-human DNA False 2016-08-24 ENCODE 1, 2 ENCFF001TDO, ENCFF348QEP, ENCFF525BTB, ENCFF617HUR 507212 ENCODE Processing Pipeline 2732be2073a35bea7c8e899b526ee7f5 https://www.encodeproject.org/files/ENCFF266KLW/@@download/ENCFF266KLW.bed.gz hg19 released mild to moderate bottlenecking, low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF177FZU bed narrowPeak optimal idr thresholded peaks ENCSR848YWD ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZMYM3-human DNA False 2016-09-23 ENCODE 1, 2 ENCFF001TDO, ENCFF136ODS, ENCFF575WAU, ENCFF629JUA 201045 ENCODE Processing Pipeline f15f87c10854c7ddee174962575bc02e https://www.encodeproject.org/files/ENCFF177FZU/@@download/ENCFF177FZU.bed.gz hg19 released low read depth, antibody characterized with exemption, mixed read lengths ENCFF003GNY bed narrowPeak optimal idr thresholded peaks ENCSR853ADA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NRF1-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF436LYU, ENCFF518DDL, ENCFF533OLJ 280925 ENCODE Processing Pipeline c43e409d329170937ef998c5d5e77be0 https://www.encodeproject.org/files/ENCFF003GNY/@@download/ENCFF003GNY.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF059ONJ bed narrowPeak optimal idr thresholded peaks ENCSR390VGH ChIP-seq EFO:0002067 K562 cell line Homo sapiens MNT-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF191KTX, ENCFF260JMM, ENCFF431KXB 698405 ENCODE Processing Pipeline b90c66a28237946beae947f6c6d02cdd https://www.encodeproject.org/files/ENCFF059ONJ/@@download/ENCFF059ONJ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF447FPV bed narrowPeak optimal idr thresholded peaks ENCSR231YFE ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZBTB33-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF515ZCN, ENCFF613ONR, ENCFF684BFS 172266 ENCODE Processing Pipeline b97a0af53cba492b881017ed8ba0ea15 https://www.encodeproject.org/files/ENCFF447FPV/@@download/ENCFF447FPV.bed.gz hg19 released borderline replicate concordance ENCFF587EOD bed narrowPeak optimal idr thresholded peaks ENCSR006WUS ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NEUROD1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF013MRQ, ENCFF503OBN, ENCFF512ZVD 119114 ENCODE Processing Pipeline 05c041dc76a925fa1f284c6192e9941c https://www.encodeproject.org/files/ENCFF587EOD/@@download/ENCFF587EOD.bed.gz hg19 released borderline replicate concordance, low read depth experiment not submitted to GEO partially characterized antibody ENCFF693JHE bed narrowPeak optimal idr thresholded peaks ENCSR903ELW ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CREM-human DNA False 2016-08-24 ENCODE 1, 2 ENCFF001TDO, ENCFF029FHZ, ENCFF467KJE, ENCFF997CFJ 519466 ENCODE Processing Pipeline d6588d01138beb53cf9323ee986d3fd8 https://www.encodeproject.org/files/ENCFF693JHE/@@download/ENCFF693JHE.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF233DOW bed narrowPeak optimal idr thresholded peaks ENCSR635OSG ChIP-seq UBERON:0002107 liver tissue Homo sapiens RAD21-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF501YCY, ENCFF654DFC, ENCFF800RTH 385302 ENCODE Processing Pipeline 4a40fd4a80e95f2166f4d6e2694c136a https://www.encodeproject.org/files/ENCFF233DOW/@@download/ENCFF233DOW.bed.gz hg19 released low read length, antibody characterized with exemption, inconsistent target of control experiment experiment not submitted to GEO missing input control ENCFF108ZTV bed narrowPeak optimal idr thresholded peaks ENCSR917QNE ChIP-seq UBERON:0002107 liver tissue Homo sapiens RAD21-human DNA False 2016-10-12 ENCODE 1, 2 ENCFF001TDO, ENCFF044MZF, ENCFF727LYG, ENCFF846YGT 1008002 ENCODE Processing Pipeline 524494eb4a5d531f9c8a7c43202a4027 https://www.encodeproject.org/files/ENCFF108ZTV/@@download/ENCFF108ZTV.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF675ZHC bed narrowPeak optimal idr thresholded peaks ENCSR634ZGP ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens UBTF-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF149RTO, ENCFF312HIY, ENCFF607MHD 19622 ENCODE Processing Pipeline 9c7c4f4820d59882e08fa26874ded8ba https://www.encodeproject.org/files/ENCFF675ZHC/@@download/ENCFF675ZHC.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity ENCFF173VKA bed narrowPeak optimal idr thresholded peaks ENCSR125ZYC ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens eGFP-KLF9-human DNA False 2016-06-13 ENCODE 3, 4 ENCFF001TDO, ENCFF328SGB, ENCFF517BWM, ENCFF667SOI 295179 ENCODE Processing Pipeline 458c3469b2c62eeda6604910e45cbd66 https://www.encodeproject.org/files/ENCFF173VKA/@@download/ENCFF173VKA.bed.gz hg19 released control low read depth, low read depth, missing genetic modification characterization ENCFF693FRV bed narrowPeak optimal idr thresholded peaks ENCSR196HGZ ChIP-seq UBERON:0002107 liver tissue Homo sapiens JUND-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF063GQS, ENCFF567PTY, ENCFF755MSZ 394305 ENCODE Processing Pipeline 433d0c39ff3942ba18f059f8a4b159d1 https://www.encodeproject.org/files/ENCFF693FRV/@@download/ENCFF693FRV.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption biological replicates with identical biosample ENCFF340PPI bed narrowPeak optimal idr thresholded peaks ENCSR695EQB ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF24-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF309SZA, ENCFF720BVJ, ENCFF924XOY 530134 ENCODE Processing Pipeline 9a398398d2c9211d4896d977bf907b72 https://www.encodeproject.org/files/ENCFF340PPI/@@download/ENCFF340PPI.bed.gz hg19 released antibody characterized with exemption ENCFF884GAH bed narrowPeak optimal idr thresholded peaks ENCSR094ZCF ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens eGFP-CEBPG-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF223YLF, ENCFF381BVK, ENCFF482DDO 234617 ENCODE Processing Pipeline 16716888547d8fbfce198b63ad9fb09b https://www.encodeproject.org/files/ENCFF884GAH/@@download/ENCFF884GAH.bed.gz hg19 released control low read depth, missing genetic modification characterization ENCFF851HUJ bed narrowPeak optimal idr thresholded peaks ENCSR994YLZ ChIP-seq UBERON:0002107 liver tissue Homo sapiens YY1-human DNA False 2016-03-31 ENCODE 1, 2 ENCFF001TDO, ENCFF435XEZ, ENCFF683XUE, ENCFF917NOB 536405 ENCODE Processing Pipeline b5663d4401ea20f7753e2b2485e7e4ae https://www.encodeproject.org/files/ENCFF851HUJ/@@download/ENCFF851HUJ.bed.gz hg19 released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF493ABN bed narrowPeak optimal idr thresholded peaks ENCSR998AJK ChIP-seq EFO:0002067 K562 cell line Homo sapiens NRF1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF113EKC, ENCFF288BMB, ENCFF406JKC 684973 ENCODE Processing Pipeline d5fff8c03ee7b8067da264cb490f4327 https://www.encodeproject.org/files/ENCFF493ABN/@@download/ENCFF493ABN.bed.gz hg19 released mild to moderate bottlenecking ENCFF887LHM bed narrowPeak optimal idr thresholded peaks ENCSR617RSQ ChIP-seq EFO:0002074 PC-3 cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF582UCY, ENCFF724ZSR, ENCFF853YEV 72796 ENCODE Processing Pipeline 31cf866fcc209e6d4489baee92e9fcd2 https://www.encodeproject.org/files/ENCFF887LHM/@@download/ENCFF887LHM.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF074EZL bed narrowPeak optimal idr thresholded peaks ENCSR085QEV ChIP-seq EFO:0002067 K562 cell line Homo sapiens NBN-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF021DHZ, ENCFF032UMZ, ENCFF650HMR 321865 ENCODE Processing Pipeline 7e52fb41f5a8121abd5a3b5a07f42747 https://www.encodeproject.org/files/ENCFF074EZL/@@download/ENCFF074EZL.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF328IOZ bed narrowPeak optimal idr thresholded peaks ENCSR886KKK ChIP-seq CL:0000103 bipolar neuron in vitro differentiated cells Homo sapiens doxycycline hyclate 0.5 μg/mL 4 day EZH2phosphoT487-human DNA False 2016-11-23 ENCODE 1, 2 ENCFF001TDO, ENCFF488KHJ, ENCFF625OET, ENCFF957ZSV 682251 ENCODE Processing Pipeline d07cb5c747bbb0c732e3f46f2e793a4b https://www.encodeproject.org/files/ENCFF328IOZ/@@download/ENCFF328IOZ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption NTR biosample ENCFF203REX bed narrowPeak optimal idr thresholded peaks ENCSR872BOU ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens FOXK2-human DNA False 2016-11-18 ENCODE 1, 2 ENCFF001TDO, ENCFF355FZF, ENCFF628SZN, ENCFF898EEY 40876 ENCODE Processing Pipeline 42a3aa6efd4c39b384ad98bd78994d4b https://www.encodeproject.org/files/ENCFF203REX/@@download/ENCFF203REX.bed.gz hg19 released mild to moderate bottlenecking ENCFF862SRI bed narrowPeak optimal idr thresholded peaks ENCSR736BUG ChIP-seq UBERON:0002107 liver tissue Homo sapiens EGR1-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF484TJY, ENCFF560WHY, ENCFF876JTC 350114 ENCODE Processing Pipeline 1c6811d4053f35decc7973fcf5f8f7b5 https://www.encodeproject.org/files/ENCFF862SRI/@@download/ENCFF862SRI.bed.gz hg19 released low read depth, antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF189HPG bed narrowPeak optimal idr thresholded peaks ENCSR098XMN ChIP-seq UBERON:0002107 liver tissue Homo sapiens RXRA-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF183ZZZ, ENCFF255SKA, ENCFF515RCQ 1202043 ENCODE Processing Pipeline c170b33e7b6fce92b71adc330e097600 https://www.encodeproject.org/files/ENCFF189HPG/@@download/ENCFF189HPG.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF272ULO bed narrowPeak optimal idr thresholded peaks ENCSR490LWA ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-CEBPG-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF183FOU, ENCFF335AYY, ENCFF880AEL 839761 ENCODE Processing Pipeline 29d7e21f3c25f41bd7185514faa49553 https://www.encodeproject.org/files/ENCFF272ULO/@@download/ENCFF272ULO.bed.gz hg19 released missing genetic modification characterization ENCFF513RIQ bed narrowPeak optimal idr thresholded peaks ENCSR764CZW ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF217-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF021SAT, ENCFF589PUL, ENCFF736WSI 393714 ENCODE Processing Pipeline d44225226240074d5eaa115e9fe46731 https://www.encodeproject.org/files/ENCFF513RIQ/@@download/ENCFF513RIQ.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF244ORA bed narrowPeak optimal idr thresholded peaks ENCSR681WHQ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ETS1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF338MRR, ENCFF749DAY, ENCFF771MQQ 165448 ENCODE Processing Pipeline 0915fff499818a173ad96b6a1787bbb4 https://www.encodeproject.org/files/ENCFF244ORA/@@download/ENCFF244ORA.bed.gz hg19 released low read length experiment not submitted to GEO partially characterized antibody ENCFF162RSN bed narrowPeak optimal idr thresholded peaks ENCSR701AQS ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF592-human DNA False 2016-10-31 ENCODE 1, 2 ENCFF001TDO, ENCFF458XHM, ENCFF824NFX, ENCFF844ATW 146581 ENCODE Processing Pipeline 7926bf331b2624cf38b2085c98494160 https://www.encodeproject.org/files/ENCFF162RSN/@@download/ENCFF162RSN.bed.gz hg19 released antibody characterized with exemption ENCFF313TUJ bed narrowPeak optimal idr thresholded peaks ENCSR423RTK ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GATA3-human DNA False 2016-10-26 ENCODE 1, 2 ENCFF001TDO, ENCFF161DQL, ENCFF863GRL, ENCFF874LLH 1016007 ENCODE Processing Pipeline 295d315f78e8a854456cd97621e2911d https://www.encodeproject.org/files/ENCFF313TUJ/@@download/ENCFF313TUJ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF120WOF bed narrowPeak optimal idr thresholded peaks ENCSR845BCL ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ZNF639-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF433SFB, ENCFF543QKR, ENCFF816KBT 407319 ENCODE Processing Pipeline ad9c782b246e9bfbb2a00cdbb89a7885 https://www.encodeproject.org/files/ENCFF120WOF/@@download/ENCFF120WOF.bed.gz hg19 released low read depth, missing genetic modification characterization ENCFF922GXT bed narrowPeak optimal idr thresholded peaks ENCSR986XYK ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens PKNOX1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF117BUH, ENCFF648CSH, ENCFF687IUI 555528 ENCODE Processing Pipeline dcc62a783ecd9b7707f05d42b9c52d1a https://www.encodeproject.org/files/ENCFF922GXT/@@download/ENCFF922GXT.bed.gz hg19 released ENCFF063WXY bed narrowPeak optimal idr thresholded peaks ENCSR793HVL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens E2F8-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF437MOX, ENCFF482LKM, ENCFF706SMS 134101 ENCODE Processing Pipeline 4c972067fd18a0101bf8d3c87a5f66f9 https://www.encodeproject.org/files/ENCFF063WXY/@@download/ENCFF063WXY.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity experiment not submitted to GEO partially characterized antibody ENCFF562JDH bed narrowPeak optimal idr thresholded peaks ENCSR075HTM ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDAC2-human DNA False 2016-10-31 ENCODE 1, 2 ENCFF001TDO, ENCFF074FFL, ENCFF810MGC, ENCFF888AZU 563260 ENCODE Processing Pipeline cc91f30f2f516fcd7c689ded645811d5 https://www.encodeproject.org/files/ENCFF562JDH/@@download/ENCFF562JDH.bed.gz hg19 released mild to moderate bottlenecking ENCFF129AXO bed narrowPeak optimal idr thresholded peaks ENCSR864KNH ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens YBX1-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF342POD, ENCFF588PWO, ENCFF820VNX 65925 ENCODE Processing Pipeline bb0020b88970e0f9422e3ea7aa6589dc https://www.encodeproject.org/files/ENCFF129AXO/@@download/ENCFF129AXO.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF051JAE bed narrowPeak optimal idr thresholded peaks ENCSR096KWU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF207-human DNA False 2016-09-01 ENCODE 1, 2 ENCFF001TDO, ENCFF454VVC, ENCFF517DCO, ENCFF669TVR 82712 ENCODE Processing Pipeline 8a2fc35aff0d987b23d18f62f4c51018 https://www.encodeproject.org/files/ENCFF051JAE/@@download/ENCFF051JAE.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF178MOP bed narrowPeak optimal idr thresholded peaks ENCSR000FCD ChIP-seq EFO:0002067 K562 cell line Homo sapiens SMAD5-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF131YKB, ENCFF235FTG, ENCFF875TQG 398842 ENCODE Processing Pipeline 8793c337b4cbb250f1ea3226f4282427 https://www.encodeproject.org/files/ENCFF178MOP/@@download/ENCFF178MOP.bed.gz hg19 released antibody characterized with exemption ENCFF235RIU bed narrowPeak optimal idr thresholded peaks ENCSR876UYH ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZHX2-human DNA False 2016-11-08 ENCODE 1, 2 ENCFF001TDO, ENCFF128RLF, ENCFF386GSB, ENCFF487NKY 141623 ENCODE Processing Pipeline dc7415cabbd37772afab2cd1348c825c https://www.encodeproject.org/files/ENCFF235RIU/@@download/ENCFF235RIU.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF973LDQ bed narrowPeak optimal idr thresholded peaks ENCSR099NCH ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF24-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF131ZOO, ENCFF716AIG, ENCFF877PNB 405803 ENCODE Processing Pipeline 5aced2d7e389eb5908524ecfd6ae9e02 https://www.encodeproject.org/files/ENCFF973LDQ/@@download/ENCFF973LDQ.bed.gz hg19 released low read depth ENCFF457PCA bed narrowPeak optimal idr thresholded peaks ENCSR656MXA ChIP-seq NTR:0000711 neural progenitor cell in vitro differentiated cells Homo sapiens EZH2phosphoT487-human DNA False 2017-02-03 ENCODE 1, 2 ENCFF001TDO, ENCFF275QAK, ENCFF624UCY, ENCFF915JWV 398387 ENCODE Processing Pipeline f73657ee4c68fe21fffa416f781b37f1 https://www.encodeproject.org/files/ENCFF457PCA/@@download/ENCFF457PCA.bed.gz hg19 released antibody characterized with exemption NTR biosample ENCFF567MGV bed narrowPeak optimal idr thresholded peaks ENCSR465XQW ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF217-human DNA False 2017-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF260SLH, ENCFF931OYK, ENCFF959GOJ 582289 ENCODE Processing Pipeline cc41dcfc4a3489a23dc37698413157be https://www.encodeproject.org/files/ENCFF567MGV/@@download/ENCFF567MGV.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF961BQJ bed narrowPeak optimal idr thresholded peaks ENCSR503VTG ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF24-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF020XZH, ENCFF239APD, ENCFF372IMH 262129 ENCODE Processing Pipeline 4b9cc48324b14cbed91146b560fc8b98 https://www.encodeproject.org/files/ENCFF961BQJ/@@download/ENCFF961BQJ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF481WGW bed narrowPeak optimal idr thresholded peaks ENCSR336DXE ChIP-seq EFO:0002067 K562 cell line Homo sapiens SKIL-human DNA False 2017-06-29 ENCODE 2, 3 ENCFF001TDO, ENCFF264IPL, ENCFF476KBA, ENCFF501IBL 449348 ENCODE Processing Pipeline 9d5b80adbb13a11fc2daf31c2c04992c https://www.encodeproject.org/files/ENCFF481WGW/@@download/ENCFF481WGW.bed.gz hg19 released mild to moderate bottlenecking ENCFF002CUL bed narrowPeak optimal idr thresholded peaks ENCSR000EDU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MXI1-human DNA see document see document False 2012-08-20 ENCODE 521816 ENCODE Consortium Analysis Working Group abb524e774342f5ff70c2f52ffe5ca43 https://www.encodeproject.org/files/ENCFF002CUL/@@download/ENCFF002CUL.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample, missing derived_from ENCFF556PIY bed narrowPeak optimal idr thresholded peaks ENCSR000DYS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens JUND-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF033WHB, ENCFF435ICE, ENCFF811UJD 138991 ENCODE Processing Pipeline c91d4953e458d7a3d972d8ce9494ff67 https://www.encodeproject.org/files/ENCFF556PIY/@@download/ENCFF556PIY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, inconsistent target of control experiment biological replicates with identical biosample ENCFF946MYA bed narrowPeak optimal idr thresholded peaks ENCSR000BJJ ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF458KOT, ENCFF639APX, ENCFF644HHB 46236 ENCODE Processing Pipeline e416fd7813f52a1578336e19c89685f0 https://www.encodeproject.org/files/ENCFF946MYA/@@download/ENCFF946MYA.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample control insufficient read depth, insufficient replicate concordance ENCFF002CQN bed narrowPeak optimal idr thresholded peaks ENCSR000EBM ChIP-seq EFO:0005351 GM19193 cell line Homo sapiens tumor necrosis factor 25 ng/mL 6 hour RELA-human DNA see document see document False 2011-10-29 ENCODE 132471 ENCODE Consortium Analysis Working Group d83a56196c352fed47578071ddf43b40 https://www.encodeproject.org/files/ENCFF002CQN/@@download/ENCFF002CQN.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF455HXN bed narrowPeak optimal idr thresholded peaks ENCSR412YGM ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZSCAN29-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF003TOD, ENCFF306UPG, ENCFF781FBO 142613 ENCODE Processing Pipeline 9e9e89c3678bd6eabbfa0df644c7f166 https://www.encodeproject.org/files/ENCFF455HXN/@@download/ENCFF455HXN.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF658MKE bed narrowPeak optimal idr thresholded peaks ENCSR460LGH ChIP-seq EFO:0006365 C4-2B cell line Homo sapiens CTCF-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF328CFX, ENCFF465DTB, ENCFF508LBP 1695710 ENCODE Processing Pipeline 262873360f58bf6d1bee505e706eb21c https://www.encodeproject.org/files/ENCFF658MKE/@@download/ENCFF658MKE.bed.gz hg19 released mild to moderate bottlenecking ENCFF398FBV bed narrowPeak optimal idr thresholded peaks ENCSR000BGB ChIP-seq EFO:0002860 SK-N-MC cell line Homo sapiens FOXP2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF510WZL, ENCFF718CML, ENCFF954MNX 185148 ENCODE Processing Pipeline efd800edbc1a0fba7b1c1a1ec8fb415d https://www.encodeproject.org/files/ENCFF398FBV/@@download/ENCFF398FBV.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth control extremely low read depth, extremely low read length ENCFF055NJR bed narrowPeak optimal idr thresholded peaks ENCSR278SQL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NBN-human DNA False 2016-08-24 ENCODE 1, 2 ENCFF001TDO, ENCFF174HNI, ENCFF211SVA, ENCFF635TWM 704612 ENCODE Processing Pipeline 983d50b2025e7cdf2bf584b28e2275d6 https://www.encodeproject.org/files/ENCFF055NJR/@@download/ENCFF055NJR.bed.gz hg19 released ENCFF643OWO bed narrowPeak optimal idr thresholded peaks ENCSR859FDL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF687-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF052WWT, ENCFF348CSG, ENCFF665KNY 594294 ENCODE Processing Pipeline e97fb90edf8b142381499be4561ffb6e https://www.encodeproject.org/files/ENCFF643OWO/@@download/ENCFF643OWO.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF132QLW bed narrowPeak optimal idr thresholded peaks ENCSR145BHD ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NFRKB-human DNA False 2017-06-29 ENCODE 3, 4 ENCFF001TDO, ENCFF205IWA, ENCFF281WBT, ENCFF724KFJ 47424 ENCODE Processing Pipeline 5a36af6c01b964b6983e7d773ad1b220 https://www.encodeproject.org/files/ENCFF132QLW/@@download/ENCFF132QLW.bed.gz hg19 released ENCFF002CEL bed narrowPeak optimal idr thresholded peaks ENCSR000AKO ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1231983 ENCODE Consortium Analysis Working Group 7ddb20610be6d90b16f37e167c79f019 https://www.encodeproject.org/files/ENCFF002CEL/@@download/ENCFF002CEL.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, mixed read lengths missing derived_from insufficient read depth ENCFF949QZO bed narrowPeak optimal idr thresholded peaks ENCSR924TVL ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens RFX5-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF366JFG, ENCFF376EFD, ENCFF458VAF 216700 ENCODE Processing Pipeline d9edd7a6a711bbc6213e1cd02d1230f2 https://www.encodeproject.org/files/ENCFF949QZO/@@download/ENCFF949QZO.bed.gz hg19 released antibody characterized with exemption ENCFF415WEH bed narrowPeak optimal idr thresholded peaks ENCSR659LJJ ChIP-seq EFO:0001086 A549 cell line Homo sapiens HDAC2-human DNA False 2016-11-23 ENCODE 1, 2 ENCFF001TDO, ENCFF047HRL, ENCFF480BUU, ENCFF869FPC 69758 ENCODE Processing Pipeline e570ad6a282afc9b551d1bc3c785260e https://www.encodeproject.org/files/ENCFF415WEH/@@download/ENCFF415WEH.bed.gz hg19 released missing control alignments ENCFF849UJR bed narrowPeak optimal idr thresholded peaks ENCSR638QYO ChIP-seq EFO:0001086 A549 cell line Homo sapiens SREBF2-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF373ECD, ENCFF757QKH, ENCFF945PVC 15537 ENCODE Processing Pipeline 18ce94b154e37d7126b3dabeec5e01e6 https://www.encodeproject.org/files/ENCFF849UJR/@@download/ENCFF849UJR.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity ENCFF671BJT bed narrowPeak optimal idr thresholded peaks ENCSR465VLK ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens FOXK2-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF462LEE, ENCFF500PCI, ENCFF610BOW 38217 ENCODE Processing Pipeline ad302231cc0be974b9752e50205047a1 https://www.encodeproject.org/files/ENCFF671BJT/@@download/ENCFF671BJT.bed.gz hg19 released borderline replicate concordance ENCFF573ALP bed narrowPeak optimal idr thresholded peaks ENCSR334KIQ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens SP1-human DNA False 2016-10-31 ENCODE 1, 2 ENCFF001TDO, ENCFF894JDZ, ENCFF894RIX, ENCFF904OAW 35549 ENCODE Processing Pipeline e3b333943669cf298b44651490ef0df4 https://www.encodeproject.org/files/ENCFF573ALP/@@download/ENCFF573ALP.bed.gz hg19 released ENCFF164EJE bed narrowPeak optimal idr thresholded peaks ENCSR560BUE ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2017-10-19 ENCODE 1, 2 ENCFF001TDO, ENCFF086WBN, ENCFF724MMC, ENCFF849TKV 948209 ENCODE Processing Pipeline 1dfc11608ac341e8e3002b060457b7b6 https://www.encodeproject.org/files/ENCFF164EJE/@@download/ENCFF164EJE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF146HGZ bed narrowPeak optimal idr thresholded peaks ENCSR435OQD ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZFX-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF222IPA, ENCFF340IJR, ENCFF795HRT 453992 ENCODE Processing Pipeline 5b42ec5877c4a8ed087f9056524528d1 https://www.encodeproject.org/files/ENCFF146HGZ/@@download/ENCFF146HGZ.bed.gz hg19 released borderline replicate concordance NTR biosample ENCFF949EAE bed narrowPeak optimal idr thresholded peaks ENCSR894SXR ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TCF12-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF208MYK, ENCFF378WXQ, ENCFF661IHD 5699 ENCODE Processing Pipeline ce4bb6cb1145b13af954783f501088d3 https://www.encodeproject.org/files/ENCFF949EAE/@@download/ENCFF949EAE.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF134NMW bed narrowPeak optimal idr thresholded peaks ENCSR415TXN ChIP-seq EFO:0002067 K562 cell line Homo sapiens NONO-human DNA SDS formaldehyde False 2017-02-27 ENCODE 1, 2 ENCFF001TDO, ENCFF028TZK, ENCFF609LOZ, ENCFF882WGE 90103 ENCODE Processing Pipeline e27dcf77f1ba6a47765799b317b359ae https://www.encodeproject.org/files/ENCFF134NMW/@@download/ENCFF134NMW.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF265NSP bed narrowPeak optimal idr thresholded peaks ENCSR979FQP ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GATAD2B-human DNA False 2017-09-29 ENCODE 1, 2 ENCFF001TDO, ENCFF042JUH, ENCFF056MRN, ENCFF930UBG 199333 ENCODE Processing Pipeline 3504216ffa027cded0fa19b18135462b https://www.encodeproject.org/files/ENCFF265NSP/@@download/ENCFF265NSP.bed.gz hg19 released ENCFF685KAG bed narrowPeak optimal idr thresholded peaks ENCSR290MUH ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-GABPA-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF026SKI, ENCFF835LBQ, ENCFF845TET 590608 ENCODE Processing Pipeline 2642e3d21c71e17716b79b0496bbf05b https://www.encodeproject.org/files/ENCFF685KAG/@@download/ENCFF685KAG.bed.gz hg19 released low read depth, missing genetic modification characterization ENCFF276KYQ bed narrowPeak optimal idr thresholded peaks ENCSR534VHI ChIP-seq EFO:0007950 GM23338 induced pluripotent stem cell line Homo sapiens ETS1-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF389SGB, ENCFF784MYN, ENCFF824HYC 188145 ENCODE Processing Pipeline fc36640405c7258cce065ca68d02f2fc https://www.encodeproject.org/files/ENCFF276KYQ/@@download/ENCFF276KYQ.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption missing control alignments ENCFF704ZYN bed narrowPeak optimal idr thresholded peaks ENCSR437GBJ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFATC3-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF452APP, ENCFF473OII, ENCFF549TIS 449441 ENCODE Processing Pipeline d57b85ace159f8e7ba3cdff45e9b3338 https://www.encodeproject.org/files/ENCFF704ZYN/@@download/ENCFF704ZYN.bed.gz hg19 released mild to moderate bottlenecking, inconsistent platforms, moderate library complexity experiment not submitted to GEO poor library complexity, severe bottlenecking, partially characterized antibody ENCFF066XDW bed narrowPeak optimal idr thresholded peaks ENCSR000DZA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MAZ-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF007UID, ENCFF138BYH, ENCFF440OBY 438480 ENCODE Processing Pipeline 819540d756d42218522ec2e8fd9c0b87 https://www.encodeproject.org/files/ENCFF066XDW/@@download/ENCFF066XDW.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF713MCF bed narrowPeak optimal idr thresholded peaks ENCSR601OGE ChIP-seq UBERON:0002107 liver tissue Homo sapiens HNF4A-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF022XIX, ENCFF240XXW, ENCFF839MCU 1254968 ENCODE Processing Pipeline 2054296572380b63d6dedec1cf356f04 https://www.encodeproject.org/files/ENCFF713MCF/@@download/ENCFF713MCF.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF804UDG bed narrowPeak optimal idr thresholded peaks ENCSR837GTK ChIP-seq UBERON:0002107 liver tissue Homo sapiens JUND-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF301CFJ, ENCFF373EUK, ENCFF436DJC 621826 ENCODE Processing Pipeline 4831345a4a86188eac653f2ee5b01725 https://www.encodeproject.org/files/ENCFF804UDG/@@download/ENCFF804UDG.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF493FED bed narrowPeak optimal idr thresholded peaks ENCSR000ARI ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF199MPQ, ENCFF670QJS, ENCFF677XOS 108726 ENCODE Processing Pipeline 9910bb382e3170e3889630548487d0bb https://www.encodeproject.org/files/ENCFF493FED/@@download/ENCFF493FED.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF387LTN bed narrowPeak optimal idr thresholded peaks ENCSR000EZV ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 6.0 hour MYC-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF028OCG, ENCFF837BDB, ENCFF951BWR 214182 ENCODE Processing Pipeline 7f880cffb36b0f56b3b62739e6b4b1b4 https://www.encodeproject.org/files/ENCFF387LTN/@@download/ENCFF387LTN.bed.gz hg19 released control low read depth, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF085HTY bed narrowPeak optimal idr thresholded peaks ENCSR000BPJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTCF-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF235AXH, ENCFF443OXB, ENCFF815GMT 795526 ENCODE Processing Pipeline ef53728caa8d0b461eed1f1fd335edf4 https://www.encodeproject.org/files/ENCFF085HTY/@@download/ENCFF085HTY.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF265QRY bed narrowPeak optimal idr thresholded peaks ENCSR000EIA ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens MXI1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF194TDU, ENCFF371MFR, ENCFF970VRK 704022 ENCODE Processing Pipeline 3d45d307ba38c7aae59c8bf33021fc47 https://www.encodeproject.org/files/ENCFF265QRY/@@download/ENCFF265QRY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF547POU bed narrowPeak optimal idr thresholded peaks ENCSR000BLW ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens EP300-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF397JOR, ENCFF906ESV, ENCFF908HDQ 549606 ENCODE Processing Pipeline 413e4eb5d23e404dfb66b7c3d8069a71 https://www.encodeproject.org/files/ENCFF547POU/@@download/ENCFF547POU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF957CWW bed narrowPeak optimal idr thresholded peaks ENCSR000EXP ChIP-seq CL:0000765 erythroblast primary cell Homo sapiens GATA1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF091ANC, ENCFF330USX, ENCFF372YKO 613178 ENCODE Processing Pipeline e9169de25a7d1181ae006801678cc91c https://www.encodeproject.org/files/ENCFF957CWW/@@download/ENCFF957CWW.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking ENCFF334FKO bed narrowPeak optimal idr thresholded peaks ENCSR893QWP ChIP-seq UBERON:0002107 liver tissue Homo sapiens REST-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF363JNV, ENCFF506HHV, ENCFF592OPP 346822 ENCODE Processing Pipeline c1655be4d3dc99d5b6dc81ee253bcce4 https://www.encodeproject.org/files/ENCFF334FKO/@@download/ENCFF334FKO.bed.gz hg19 released mild to moderate bottlenecking, low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF874DDR bed narrowPeak optimal idr thresholded peaks ENCSR000DMY ChIP-seq EFO:0002939 medulloblastoma cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF012GOG, ENCFF525QBA, ENCFF550YRO 699291 ENCODE Processing Pipeline 09f2bc62227b28b0550ce5999dd49d02 https://www.encodeproject.org/files/ENCFF874DDR/@@download/ENCFF874DDR.bed.gz hg19 released control low read depth, mild to moderate bottlenecking, low read depth biological replicates with identical biosample missing control alignments ENCFF667URP bed narrowPeak optimal idr thresholded peaks ENCSR000BLT ChIP-seq EFO:0002786 GM12892 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF311HXH, ENCFF434TLG, ENCFF797ZRE 329888 ENCODE Processing Pipeline 691ee9a84e6688bc1a23a04fcd3fb199 https://www.encodeproject.org/files/ENCFF667URP/@@download/ENCFF667URP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF557DSM bed narrowPeak optimal idr thresholded peaks ENCSR000EWF ChIP-seq EFO:0002067 K562 cell line Homo sapiens YY1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF211PND, ENCFF228AYO, ENCFF899XEM 93049 ENCODE Processing Pipeline cf8ffec94a9b83f40812443c565a6a17 https://www.encodeproject.org/files/ENCFF557DSM/@@download/ENCFF557DSM.bed.gz hg19 released borderline replicate concordance biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF566FVB bed narrowPeak optimal idr thresholded peaks ENCSR205FOW ChIP-seq UBERON:0002107 liver tissue Homo sapiens ATF3-human DNA False 2016-03-31 ENCODE 1, 2 ENCFF001TDO, ENCFF025EPQ, ENCFF515NYK, ENCFF811WQQ 307540 ENCODE Processing Pipeline 27f4568230f4e95c89aa289b352058cd https://www.encodeproject.org/files/ENCFF566FVB/@@download/ENCFF566FVB.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF971QHN bed narrowPeak optimal idr thresholded peaks ENCSR297GII ChIP-seq UBERON:0002107 liver tissue Homo sapiens HNF4G-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF003GWJ, ENCFF129GGF, ENCFF651MBI 384070 ENCODE Processing Pipeline b2dc6635b5a638f683ecc6f1d4144373 https://www.encodeproject.org/files/ENCFF971QHN/@@download/ENCFF971QHN.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF126PNX bed narrowPeak optimal idr thresholded peaks ENCSR324RCI ChIP-seq UBERON:0002107 liver tissue Homo sapiens FOXA1-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF363RKC, ENCFF971SJB, ENCFF972ILN 336869 ENCODE Processing Pipeline 6d717898050610295a501877bd125954 https://www.encodeproject.org/files/ENCFF126PNX/@@download/ENCFF126PNX.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity, antibody characterized with exemption biological replicates with identical biosample ENCFF693PZH bed narrowPeak optimal idr thresholded peaks ENCSR619IUE ChIP-seq CL:0000103 bipolar neuron in vitro differentiated cells Homo sapiens doxycycline hyclate 0.5 μg/mL 4 day CTCF-human DNA False 2016-10-27 ENCODE 1, 2 ENCFF001TDO, ENCFF263PBF, ENCFF682TFX, ENCFF721XMZ 956798 ENCODE Processing Pipeline 204ad61bcdc9e26628e1deafb30a2fed https://www.encodeproject.org/files/ENCFF693PZH/@@download/ENCFF693PZH.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption biological replicates with identical biosample, NTR biosample ENCFF142EVF bed narrowPeak optimal idr thresholded peaks ENCSR212YKD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SKIL-human DNA False 2017-07-24 ENCODE 1, 2 ENCFF001TDO, ENCFF047ZBU, ENCFF513BIR, ENCFF922PHV 520152 ENCODE Processing Pipeline 7d07051af43759929280cae1252a92bb https://www.encodeproject.org/files/ENCFF142EVF/@@download/ENCFF142EVF.bed.gz hg19 released mild to moderate bottlenecking, low read depth, inconsistent platforms experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF017YUI bed narrowPeak optimal idr thresholded peaks ENCSR386YIH ChIP-seq UBERON:0002107 liver tissue Homo sapiens SP1-human DNA False 2018-02-08 ENCODE 1, 2 ENCFF001TDO, ENCFF027RDL, ENCFF084INO, ENCFF571PKW 1086792 ENCODE Processing Pipeline 6d927fefe02424dcffe488b1873c853e https://www.encodeproject.org/files/ENCFF017YUI/@@download/ENCFF017YUI.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF002CTK bed narrowPeak optimal idr thresholded peaks ENCSR000EVE ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens TCF7L2-human DNA see document see document False 2012-05-14 ENCODE 437958 ENCODE Consortium Analysis Working Group b6b4a4d0d1cbe37588a4d53cf3d70440 https://www.encodeproject.org/files/ENCFF002CTK/@@download/ENCFF002CTK.bed.gz hg19 released low read length, inconsistent platforms missing derived_from, biological replicates with identical biosample ENCFF274TYW bed narrowPeak optimal idr thresholded peaks ENCSR000BVO ChIP-seq EFO:0001247 T47D cell line Homo sapiens JUND-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF242EJE, ENCFF289KHP, ENCFF772MXQ 164639 ENCODE Processing Pipeline a0226d35a19d707f0c8598c8549dc61d https://www.encodeproject.org/files/ENCFF274TYW/@@download/ENCFF274TYW.bed.gz hg19 released low read depth biological replicates with identical biosample ENCFF201MOM bed narrowPeak optimal idr thresholded peaks ENCSR445QRF ChIP-seq UBERON:0002107 liver tissue Homo sapiens HNF4A-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF088ETE, ENCFF618OVE, ENCFF901DDA 1163150 ENCODE Processing Pipeline a2e668e5d2b1eee01a1e10e713d8b6b6 https://www.encodeproject.org/files/ENCFF201MOM/@@download/ENCFF201MOM.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF831MEQ bed narrowPeak optimal idr thresholded peaks ENCSR290ZOS ChIP-seq UBERON:0002107 liver tissue Homo sapiens EGR1-human DNA False 2018-02-08 ENCODE 1, 2 ENCFF001TDO, ENCFF145YNF, ENCFF618LWB, ENCFF963HHX 154457 ENCODE Processing Pipeline a9c85d1261d6986e36bde2bff9d695fc https://www.encodeproject.org/files/ENCFF831MEQ/@@download/ENCFF831MEQ.bed.gz hg19 released low read depth, antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF288UUU bed narrowPeak optimal idr thresholded peaks ENCSR636YLV ChIP-seq EFO:0001086 A549 cell line Homo sapiens MAZ-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF072HSB, ENCFF472YFZ, ENCFF542JSY 73312 ENCODE Processing Pipeline 45aa3b730ac79670ffb336af6ab340d4 https://www.encodeproject.org/files/ENCFF288UUU/@@download/ENCFF288UUU.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF840NOO bed narrowPeak optimal idr thresholded peaks ENCSR847DIT ChIP-seq UBERON:0002107 liver tissue Homo sapiens MAX-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF151FBW, ENCFF810FLM, ENCFF981QWW 547666 ENCODE Processing Pipeline 9e7471dd4ce8fad320cb14b095049694 https://www.encodeproject.org/files/ENCFF840NOO/@@download/ENCFF840NOO.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF258PIW bed narrowPeak optimal idr thresholded peaks ENCSR038GMB ChIP-seq UBERON:0002107 liver tissue Homo sapiens GABPA-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF045GWC, ENCFF556UZM, ENCFF634EKL 369257 ENCODE Processing Pipeline 95e75578d1c167b5e7e081f192c5011b https://www.encodeproject.org/files/ENCFF258PIW/@@download/ENCFF258PIW.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF688LUP bed narrowPeak optimal idr thresholded peaks ENCSR516HUP ChIP-seq UBERON:0002107 liver tissue Homo sapiens ZBTB33-human DNA False 2016-09-19 ENCODE 1, 2 ENCFF001TDO, ENCFF080EAQ, ENCFF373SRH, ENCFF582WLM 345115 ENCODE Processing Pipeline 6261d9022afb9f39ecff325f89aa7120 https://www.encodeproject.org/files/ENCFF688LUP/@@download/ENCFF688LUP.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF786DKS bed narrowPeak optimal idr thresholded peaks ENCSR310NYI ChIP-seq UBERON:0002107 liver tissue Homo sapiens FOXA2-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF047WBC, ENCFF125PLO, ENCFF474ZPF 417839 ENCODE Processing Pipeline cea1a5e5ed8c5d53eed103f964f51b28 https://www.encodeproject.org/files/ENCFF786DKS/@@download/ENCFF786DKS.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF166FRO bed narrowPeak optimal idr thresholded peaks ENCSR746XEG ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFXL1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF044ASF, ENCFF635ZSK, ENCFF763SSU 111900 ENCODE Processing Pipeline ecdcd45712ada557b780b8561c0c71c2 https://www.encodeproject.org/files/ENCFF166FRO/@@download/ENCFF166FRO.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, antibody characterized with exemption ENCFF465JKF bed narrowPeak optimal idr thresholded peaks ENCSR000EGJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens MYC-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF019DFB, ENCFF033VDX, ENCFF165VLE 538620 ENCODE Processing Pipeline 146303efe433182be7daba2298a9ffda https://www.encodeproject.org/files/ENCFF465JKF/@@download/ENCFF465JKF.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF522JRK bed narrowPeak optimal idr thresholded peaks ENCSR000EFR ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZC3H11A-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF305IJI, ENCFF547MRJ, ENCFF726OZS 51017 ENCODE Processing Pipeline 81ec05387a90d3fd3d085fdfd8e8c470 https://www.encodeproject.org/files/ENCFF522JRK/@@download/ENCFF522JRK.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF809OOE bed narrowPeak optimal idr thresholded peaks ENCSR441VHN ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens IKZF1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF413ANK, ENCFF526LHJ, ENCFF963HCJ 1251501 ENCODE Processing Pipeline 9dc6f420639e0a265f3f179b6b42713a https://www.encodeproject.org/files/ENCFF809OOE/@@download/ENCFF809OOE.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF633IHZ bed narrowPeak optimal idr thresholded peaks ENCSR036EGV ChIP-seq CL:1001606 foreskin keratinocyte primary cell Homo sapiens calcium 1.2 mM 2.5 day CTCF-human DNA formaldehyde False 2017-10-10 GGR 1, 2 ENCFF001TDO, ENCFF007ACV, ENCFF239HMM, ENCFF244MXM 1060208 ENCODE Processing Pipeline 5075db80d4e5d5c13519931167353be7 https://www.encodeproject.org/files/ENCFF633IHZ/@@download/ENCFF633IHZ.bed.gz hg19 released experiment not submitted to GEO ENCFF958VNQ bed narrowPeak optimal idr thresholded peaks ENCSR000DYE ChIP-seq EFO:0001086 A549 cell line Homo sapiens RAD21-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF067TKW, ENCFF425OPL, ENCFF907WEZ 448758 ENCODE Processing Pipeline f59819bf62d5b8f038e3dcc9d07920fb https://www.encodeproject.org/files/ENCFF958VNQ/@@download/ENCFF958VNQ.bed.gz hg19 released low read length, inconsistent platforms, inconsistent target of control experiment biological replicates with identical biosample ENCFF462CPT bed narrowPeak optimal idr thresholded peaks ENCSR492LTS ChIP-seq EFO:0002067 K562 cell line Homo sapiens BCLAF1-human DNA False 2017-02-02 ENCODE 1, 2 ENCFF001TDO, ENCFF027UPQ, ENCFF202AHW, ENCFF662CIT 61355 ENCODE Processing Pipeline e5f4357bf52033266e56f7a93118ed40 https://www.encodeproject.org/files/ENCFF462CPT/@@download/ENCFF462CPT.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF207YNL bed narrowPeak optimal idr thresholded peaks ENCSR735KEY ChIP-seq UBERON:0002107 liver tissue Homo sapiens FOXA1-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF712EUK, ENCFF841RCY, ENCFF924RTU 295835 ENCODE Processing Pipeline d9ed0e1afecb61a6948b1a641fbfa1b9 https://www.encodeproject.org/files/ENCFF207YNL/@@download/ENCFF207YNL.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF712AXK bed narrowPeak optimal idr thresholded peaks ENCSR707QWA ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR2F6-human DNA False 2016-06-28 ENCODE 1, 2 ENCFF001TDO, ENCFF106WRW, ENCFF134OVY, ENCFF604XWK 402996 ENCODE Processing Pipeline d4ef75a204c84efaad5df40feb9c957b https://www.encodeproject.org/files/ENCFF712AXK/@@download/ENCFF712AXK.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF511QHY bed narrowPeak optimal idr thresholded peaks ENCSR102KIN ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZMYM3-human DNA False 2016-10-12 ENCODE 1, 2 ENCFF001TDO, ENCFF204QNV, ENCFF438LLN, ENCFF925VOV 668402 ENCODE Processing Pipeline 2a540d117bdccfec94aa0f5dc33dc677 https://www.encodeproject.org/files/ENCFF511QHY/@@download/ENCFF511QHY.bed.gz hg19 released antibody characterized with exemption, mixed read lengths ENCFF813VLK bed narrowPeak optimal idr thresholded peaks ENCSR090ZDO ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens SUZ12-human DNA False 2016-11-18 ENCODE 1, 2 ENCFF001TDO, ENCFF230ONV, ENCFF599ICL, ENCFF761HEQ 20025 ENCODE Processing Pipeline 056a79d036d303f6d0cda17c93bb1e4f https://www.encodeproject.org/files/ENCFF813VLK/@@download/ENCFF813VLK.bed.gz hg19 released mild to moderate bottlenecking ENCFF248VHN bed narrowPeak optimal idr thresholded peaks ENCSR302AWT ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOXK2-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF037YFB, ENCFF203SUN, ENCFF732HYH 358492 ENCODE Processing Pipeline 6617b946d9b9a9e353cf71f681323126 https://www.encodeproject.org/files/ENCFF248VHN/@@download/ENCFF248VHN.bed.gz hg19 released low read depth ENCFF977MDK bed narrowPeak optimal idr thresholded peaks ENCSR000EBQ ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens BACH1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF415TPT, ENCFF502ZML, ENCFF627CTC 231168 ENCODE Processing Pipeline f0d5e3cdd99adc2c94a24de809558a54 https://www.encodeproject.org/files/ENCFF977MDK/@@download/ENCFF977MDK.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF253NXR bed narrowPeak optimal idr thresholded peaks ENCSR175SZH ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZSCAN29-human DNA False 2016-10-31 ENCODE 1, 2 ENCFF001TDO, ENCFF118YQO, ENCFF483NEI, ENCFF788QDP 323129 ENCODE Processing Pipeline ce16e91b56c848b604565d6e0c378f09 https://www.encodeproject.org/files/ENCFF253NXR/@@download/ENCFF253NXR.bed.gz hg19 released low read depth ENCFF956LMS bed narrowPeak optimal idr thresholded peaks ENCSR757EMK ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens SUZ12-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF050ZNZ, ENCFF497GTZ, ENCFF706VXW 121082 ENCODE Processing Pipeline 6ca14a532bb29b2041757fdb0d29a730 https://www.encodeproject.org/files/ENCFF956LMS/@@download/ENCFF956LMS.bed.gz hg19 released ENCFF632MBO bed narrowPeak optimal idr thresholded peaks ENCSR813DCK ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SMAD1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF057LDF, ENCFF562WIC, ENCFF916SIZ 208040 ENCODE Processing Pipeline 77c0993b8896711fa45c03a67e592c7b https://www.encodeproject.org/files/ENCFF632MBO/@@download/ENCFF632MBO.bed.gz hg19 released mild to moderate bottlenecking, low read depth experiment not submitted to GEO partially characterized antibody ENCFF103OOV bed narrowPeak optimal idr thresholded peaks ENCSR072PWP ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF24-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF593RSQ, ENCFF882PND, ENCFF956UUX 335127 ENCODE Processing Pipeline dc50267f97e94c42ba040408571a95a8 https://www.encodeproject.org/files/ENCFF103OOV/@@download/ENCFF103OOV.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF426DUB bed narrowPeak optimal idr thresholded peaks ENCSR795IYP ChIP-seq EFO:0002067 K562 cell line Homo sapiens JUNB-human DNA False 2016-03-02 ENCODE 1, 2 ENCFF001TDO, ENCFF127XOZ, ENCFF325KGM, ENCFF997SXB 95173 ENCODE Processing Pipeline 9f0888598e4c0a94620276153bf94d46 https://www.encodeproject.org/files/ENCFF426DUB/@@download/ENCFF426DUB.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF920LEU bed narrowPeak optimal idr thresholded peaks ENCSR799GOY ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens YBX1-human DNA False 2016-09-01 ENCODE 1, 2 ENCFF001TDO, ENCFF527RBD, ENCFF674AYU, ENCFF716TQR 88695 ENCODE Processing Pipeline 3294d59a75115ea2e7bba0de196a9231 https://www.encodeproject.org/files/ENCFF920LEU/@@download/ENCFF920LEU.bed.gz hg19 released antibody characterized with exemption ENCFF431CEH bed narrowPeak optimal idr thresholded peaks ENCSR264RJX ChIP-seq EFO:0007950 GM23338 induced pluripotent stem cell line Homo sapiens POU5F1-human DNA False 2016-06-16 ENCODE 1, 2 ENCFF001TDO, ENCFF142NKY, ENCFF214FTU, ENCFF916HRC 139075 ENCODE Processing Pipeline 28fb1d0f3e4fa242a8e3be631f12ab66 https://www.encodeproject.org/files/ENCFF431CEH/@@download/ENCFF431CEH.bed.gz hg19 released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF986MHU bed narrowPeak optimal idr thresholded peaks ENCSR085DDI ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFXL1-human DNA False 2016-12-05 ENCODE 1, 2 ENCFF001TDO, ENCFF297LLA, ENCFF666TVL, ENCFF804ZDO 116563 ENCODE Processing Pipeline a5428ff5fcb7004b76804e57d613d5fd https://www.encodeproject.org/files/ENCFF986MHU/@@download/ENCFF986MHU.bed.gz hg19 released ENCFF839EPV bed narrowPeak optimal idr thresholded peaks ENCSR417DKD ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NFXL1-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF447SAN, ENCFF842DAK, ENCFF875DOP 44419 ENCODE Processing Pipeline 2ab64fcc59001a92495fc446b93c8748 https://www.encodeproject.org/files/ENCFF839EPV/@@download/ENCFF839EPV.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF760HUV bed narrowPeak optimal idr thresholded peaks ENCSR932ZMX ChIP-seq EFO:0007950 GM23338 induced pluripotent stem cell line Homo sapiens CTCF-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF346PQE, ENCFF414BJO, ENCFF661MCK 1427699 ENCODE Processing Pipeline 4afa784408ac7c6d1be29f75f613ebeb https://www.encodeproject.org/files/ENCFF760HUV/@@download/ENCFF760HUV.bed.gz hg19 released mild to moderate bottlenecking, low read depth, antibody characterized with exemption NTR biosample ENCFF241JKV bed narrowPeak optimal idr thresholded peaks ENCSR303GFI ChIP-seq EFO:0002323 RWPE1 cell line Homo sapiens CTCF-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF281EIU, ENCFF605AVV, ENCFF677QYW 930122 ENCODE Processing Pipeline 0a7755c1ba62ad85da95d6f5e7f2a2ad https://www.encodeproject.org/files/ENCFF241JKV/@@download/ENCFF241JKV.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF459YEI bed narrowPeak optimal idr thresholded peaks ENCSR817HTJ ChIP-seq CL:1001606 foreskin keratinocyte primary cell Homo sapiens CTCF-human DNA formaldehyde False 2017-10-10 GGR 1, 2 ENCFF001TDO, ENCFF379YTS, ENCFF673WMU, ENCFF774PLL 1223933 ENCODE Processing Pipeline f817005605e7a1474a2e57fdfc3582b4 https://www.encodeproject.org/files/ENCFF459YEI/@@download/ENCFF459YEI.bed.gz hg19 released experiment not submitted to GEO ENCFF968EAL bed narrowPeak optimal idr thresholded peaks ENCSR353HEP ChIP-seq EFO:0002067 K562 cell line Homo sapiens TARDBP-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF027BJC, ENCFF032HCI, ENCFF139HGF 136479 ENCODE Processing Pipeline bba8e09d361ca0cf21a60e83afff4fcd https://www.encodeproject.org/files/ENCFF968EAL/@@download/ENCFF968EAL.bed.gz hg19 released low read depth ENCFF253FON bed narrowPeak optimal idr thresholded peaks ENCSR286PCG ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZBED1-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF052CCG, ENCFF259MRC, ENCFF648RRL 104275 ENCODE Processing Pipeline 5fdeef786b8622e06a21d2c820b3da97 https://www.encodeproject.org/files/ENCFF253FON/@@download/ENCFF253FON.bed.gz hg19 released ENCFF374HJR bed narrowPeak optimal idr thresholded peaks ENCSR016UEH ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TARDBP-human DNA see document see document False 2016-11-08 ENCODE 1, 2 ENCFF001TDO, ENCFF025MTA, ENCFF168RYI, ENCFF500LLP 117764 ENCODE Processing Pipeline aa3bef7e4e1504bc5d0fe6d1cb3b61b9 https://www.encodeproject.org/files/ENCFF374HJR/@@download/ENCFF374HJR.bed.gz hg19 released borderline replicate concordance, low read depth ENCFF662MVX bed narrowPeak optimal idr thresholded peaks ENCSR411UYA ChIP-seq EFO:0002067 K562 cell line Homo sapiens MTA2-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF084ILX, ENCFF605LJE, ENCFF850ENR 384677 ENCODE Processing Pipeline 21d4fc2074ca86610ddb256b957f4bfa https://www.encodeproject.org/files/ENCFF662MVX/@@download/ENCFF662MVX.bed.gz hg19 released ENCFF901JRM bed narrowPeak optimal idr thresholded peaks ENCSR736ZKL ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-ZNF148-human DNA formaldehyde False 2017-02-21 ENCODE 1, 2 ENCFF001TDO, ENCFF248EEY, ENCFF462BHV, ENCFF969JFO 68814 ENCODE Processing Pipeline f12ce089c0b22e41abf68af12c139976 https://www.encodeproject.org/files/ENCFF901JRM/@@download/ENCFF901JRM.bed.gz hg19 released missing genetic modification characterization missing control alignments ENCFF095TYO bed narrowPeak optimal idr thresholded peaks ENCSR382PVA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens GTF2F1-human DNA SDS formaldehyde False 2017-02-27 ENCODE 1, 2 ENCFF001TDO, ENCFF033KIA, ENCFF266MOP, ENCFF366ELK 110208 ENCODE Processing Pipeline 460e9f143793618480cb42863a585128 https://www.encodeproject.org/files/ENCFF095TYO/@@download/ENCFF095TYO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF193FZK bed narrowPeak optimal idr thresholded peaks ENCSR337NQP ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ESRRA-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF111XHJ, ENCFF472FKC, ENCFF484BXC 37772 ENCODE Processing Pipeline 6d8a2ae1b22bb8666ac032eee0fec1c5 https://www.encodeproject.org/files/ENCFF193FZK/@@download/ENCFF193FZK.bed.gz hg19 released borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF788CHY bed narrowPeak optimal idr thresholded peaks ENCSR856JJB ChIP-seq EFO:0007610 RWPE2 cell line Homo sapiens CTCF-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF105NHW, ENCFF282SYC, ENCFF828HUH 1817661 ENCODE Processing Pipeline 250df0fa4ddeb6f03963a6a3429bacff https://www.encodeproject.org/files/ENCFF788CHY/@@download/ENCFF788CHY.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF398TWC bed narrowPeak optimal idr thresholded peaks ENCSR792IYC ChIP-seq EFO:0002067 K562 cell line Homo sapiens BCLAF1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF002NNQ, ENCFF039VDD, ENCFF519QDT 39607 ENCODE Processing Pipeline 95c94c1100d8e4fdb273a6e4dda01157 https://www.encodeproject.org/files/ENCFF398TWC/@@download/ENCFF398TWC.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF947SUP bed narrowPeak optimal idr thresholded peaks ENCSR429CLV ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF692CDD, ENCFF734XYJ, ENCFF941MND 9304 ENCODE Processing Pipeline 6f5ef776604ae4ef6e6428c16abcc69a https://www.encodeproject.org/files/ENCFF947SUP/@@download/ENCFF947SUP.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF381SBC bed narrowPeak optimal idr thresholded peaks ENCSR784VIQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NR2C1-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF041WNR, ENCFF119UKJ, ENCFF685WLQ 198894 ENCODE Processing Pipeline 4eae90be6d7c11e1201772554bef3773 https://www.encodeproject.org/files/ENCFF381SBC/@@download/ENCFF381SBC.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF490VVG bed narrowPeak optimal idr thresholded peaks ENCSR893WSB ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDAC2-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF368EUJ, ENCFF380RMA, ENCFF399PWD 687231 ENCODE Processing Pipeline fca556d6c89db48dae7c6c046425eeb5 https://www.encodeproject.org/files/ENCFF490VVG/@@download/ENCFF490VVG.bed.gz hg19 released borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF569XCA bed narrowPeak optimal idr thresholded peaks ENCSR476BQA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NONO-human DNA False 2017-02-01 ENCODE 1, 2 ENCFF001TDO, ENCFF234DZJ, ENCFF437VMK, ENCFF875EQQ 43938 ENCODE Processing Pipeline fa06ed25bf1a2fc1f65dfe212ada330b https://www.encodeproject.org/files/ENCFF569XCA/@@download/ENCFF569XCA.bed.gz hg19 released borderline replicate concordance ENCFF038MZK bed narrowPeak optimal idr thresholded peaks ENCSR562NOP ChIP-seq EFO:0002167 DOHH2 cell line Homo sapiens EZH2phosphoT487-human DNA see document see document False 2017-01-31 ENCODE 1, 2 ENCFF001TDO, ENCFF539MLU, ENCFF669EAC, ENCFF945BEK 78237 ENCODE Processing Pipeline 0bafc2c533ebff4696c7daaefd3bf334 https://www.encodeproject.org/files/ENCFF038MZK/@@download/ENCFF038MZK.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, antibody characterized with exemption, mixed read lengths NTR biosample ENCFF445LQN bed narrowPeak optimal idr thresholded peaks ENCSR620DUQ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CREB1-human DNA False 2017-09-28 ENCODE 1, 2 ENCFF001TDO, ENCFF040JIX, ENCFF783CTL, ENCFF790WFD 851936 ENCODE Processing Pipeline 70561ac7f1ddb5a4e1c45eb02ab2b02c https://www.encodeproject.org/files/ENCFF445LQN/@@download/ENCFF445LQN.bed.gz hg19 released ENCFF776YPS bed narrowPeak optimal idr thresholded peaks ENCSR886RYH ChIP-seq EFO:0002067 K562 cell line Homo sapiens NONO-human DNA False 2017-01-31 ENCODE 3, 4 ENCFF001TDO, ENCFF324CAZ, ENCFF433ZFX, ENCFF784OAB 232581 ENCODE Processing Pipeline 5c0614ca3f5ea89ffbd81ad107a5c28e https://www.encodeproject.org/files/ENCFF776YPS/@@download/ENCFF776YPS.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF842WEF bed narrowPeak optimal idr thresholded peaks ENCSR027UFT ChIP-seq EFO:0006365 C4-2B cell line Homo sapiens ZFX-human DNA False 2017-05-18 ENCODE 1, 2 ENCFF001TDO, ENCFF647SSO, ENCFF826ULZ, ENCFF998YLT 347370 ENCODE Processing Pipeline 6f271660d54a0c592fbb46ce8ac25719 https://www.encodeproject.org/files/ENCFF842WEF/@@download/ENCFF842WEF.bed.gz hg19 released NTR biosample ENCFF698WAX bed narrowPeak optimal idr thresholded peaks ENCSR196HOM ChIP-seq CL:0002231 epithelial cell of prostate primary cell Homo sapiens CTCF-human DNA False 2017-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF276RMO, ENCFF344AQO, ENCFF759LYG 1874386 ENCODE Processing Pipeline 91702d6a98f8d9cd05674e5be55bb360 https://www.encodeproject.org/files/ENCFF698WAX/@@download/ENCFF698WAX.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF259XYR bed narrowPeak optimal idr thresholded peaks ENCSR847XGE ChIP-seq EFO:0002095 22Rv1 cell line Homo sapiens 17β-hydroxy-5α-androstan-3-one 10 nM 4 hour CTCF-human DNA False 2017-06-29 ENCODE 1, 2 ENCFF001TDO, ENCFF011GSD, ENCFF166YLC, ENCFF465IOZ 1551773 ENCODE Processing Pipeline 02a67a4ed01b96ee32b7c7c06a2bb4cb https://www.encodeproject.org/files/ENCFF259XYR/@@download/ENCFF259XYR.bed.gz hg19 released mild to moderate bottlenecking NTR biosample ENCFF052YIL bed narrowPeak optimal idr thresholded peaks ENCSR015TKV ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens BCLAF1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF593TJL, ENCFF624REB, ENCFF650KWX 5625 ENCODE Processing Pipeline d302d6e124651bc641b05621e8669fe0 https://www.encodeproject.org/files/ENCFF052YIL/@@download/ENCFF052YIL.bed.gz hg19 released mild to moderate bottlenecking ENCFF446FHX bed narrowPeak optimal idr thresholded peaks ENCSR248IMH ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NFRKB-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF610HTV, ENCFF887ZYJ, ENCFF924OFW 27172 ENCODE Processing Pipeline 662ff52d399651dc17f01ed9a22ef122 https://www.encodeproject.org/files/ENCFF446FHX/@@download/ENCFF446FHX.bed.gz hg19 released mild to moderate bottlenecking ENCFF250ZAH bed narrowPeak optimal idr thresholded peaks ENCSR812FNU ChIP-seq CL:1001606 foreskin keratinocyte primary cell Homo sapiens calcium 1.2 mM 5.5 day CTCF-human DNA formaldehyde False 2017-10-10 GGR 1, 2 ENCFF001TDO, ENCFF128OKK, ENCFF562OUS, ENCFF956IFC 1009516 ENCODE Processing Pipeline 8c4b57e46695bb74b34ca789b2be01ad https://www.encodeproject.org/files/ENCFF250ZAH/@@download/ENCFF250ZAH.bed.gz hg19 released experiment not submitted to GEO ENCFF027CYL bed narrowPeak optimal idr thresholded peaks ENCSR460XGV ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MNT-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF600NIF, ENCFF780FQB, ENCFF978HRR 23359 ENCODE Processing Pipeline 16be5a6879f034e9b5c4b6d81d2d3fdc https://www.encodeproject.org/files/ENCFF027CYL/@@download/ENCFF027CYL.bed.gz hg19 released ENCFF769GYG bed narrowPeak optimal idr thresholded peaks ENCSR807BGP ChIP-seq EFO:0002067 K562 cell line Homo sapiens MTA1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF253PLF, ENCFF387NDE, ENCFF658ZHZ 334404 ENCODE Processing Pipeline 9721f8e11cc0a98b2e92a7ee4f682542 https://www.encodeproject.org/files/ENCFF769GYG/@@download/ENCFF769GYG.bed.gz hg19 released borderline replicate concordance ENCFF443EYO bed narrowPeak optimal idr thresholded peaks ENCSR362NWP ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF24-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF395YWQ, ENCFF859ZGV, ENCFF960SGY 147195 ENCODE Processing Pipeline 7f5a9423cdb84a36e4eb1a9e4d82cc96 https://www.encodeproject.org/files/ENCFF443EYO/@@download/ENCFF443EYO.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF566YUW bed narrowPeak optimal idr thresholded peaks ENCSR173ZVL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF592-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF569JWR, ENCFF629PYS, ENCFF886RMX 226453 ENCODE Processing Pipeline e42b637c8a6e8fa11ce0322f1525c6d4 https://www.encodeproject.org/files/ENCFF566YUW/@@download/ENCFF566YUW.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF445OFX bed narrowPeak optimal idr thresholded peaks ENCSR246MLJ ChIP-seq EFO:0002095 22Rv1 cell line Homo sapiens ZFX-human DNA False 2017-06-15 ENCODE 1, 2 ENCFF001TDO, ENCFF413CDN, ENCFF865UXS, ENCFF881NRM 7060 ENCODE Processing Pipeline ab0ec33cf8865cad353c7eac9c884812 https://www.encodeproject.org/files/ENCFF445OFX/@@download/ENCFF445OFX.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption NTR biosample ENCFF763GJP bed narrowPeak optimal idr thresholded peaks ENCSR730TBC ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MNT-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF368MWT, ENCFF617PCO, ENCFF641DSK 217965 ENCODE Processing Pipeline 0416804df0cf36ce6c564ea3183bee52 https://www.encodeproject.org/files/ENCFF763GJP/@@download/ENCFF763GJP.bed.gz hg19 released ENCFF017LZE bed narrowPeak optimal idr thresholded peaks ENCSR725VFL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TCF12-human DNA False 2017-06-07 ENCODE 1, 2 ENCFF001TDO, ENCFF531FOV, ENCFF595TGO, ENCFF601WVR 290462 ENCODE Processing Pipeline 67d4968a8aa146ff684f8bb6aabb0364 https://www.encodeproject.org/files/ENCFF017LZE/@@download/ENCFF017LZE.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF802XZN bed narrowPeak optimal idr thresholded peaks ENCSR608HVP ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-KLF13-human DNA False 2016-03-02 ENCODE 1, 2 ENCFF001TDO, ENCFF119DBB, ENCFF163SYH, ENCFF367KYN 180679 ENCODE Processing Pipeline c2b97dbdcdb1a3eb640515e00cd7a237 https://www.encodeproject.org/files/ENCFF802XZN/@@download/ENCFF802XZN.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity, missing genetic modification characterization ENCFF155SPQ bed narrowPeak optimal idr thresholded peaks ENCSR315NAC ChIP-seq EFO:0002071 LNCAP cell line Homo sapiens CTCF-human DNA False 2017-06-29 ENCODE 1, 2 ENCFF001TDO, ENCFF263EYR, ENCFF930VYW, ENCFF977TIL 966701 ENCODE Processing Pipeline 9e3c6202b70ffd4857cfa6a4429b30c2 https://www.encodeproject.org/files/ENCFF155SPQ/@@download/ENCFF155SPQ.bed.gz hg19 released mild to moderate bottlenecking ENCFF144BSH bed narrowPeak optimal idr thresholded peaks ENCSR503GVO ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens ZFX-human DNA False 2017-09-07 ENCODE 1, 2 ENCFF001TDO, ENCFF437EHR, ENCFF610MUA, ENCFF939NVJ 446793 ENCODE Processing Pipeline 136660c4dfc08cf2e1a901894c44e523 https://www.encodeproject.org/files/ENCFF144BSH/@@download/ENCFF144BSH.bed.gz hg19 released NTR biosample ENCFF534CKB bed narrowPeak optimal idr thresholded peaks ENCSR839XZU ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CREM-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF263KGZ, ENCFF510TYC, ENCFF874IMP 555303 ENCODE Processing Pipeline 9bde60dc90e039a208a7b9b7abedd50c https://www.encodeproject.org/files/ENCFF534CKB/@@download/ENCFF534CKB.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF305ICK bed narrowPeak optimal idr thresholded peaks ENCSR501DKS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TCF7-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF508MRO, ENCFF925ZGX, ENCFF988AWI 177224 ENCODE Processing Pipeline a4d821726cb81b6e654150bb39ba9b05 https://www.encodeproject.org/files/ENCFF305ICK/@@download/ENCFF305ICK.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF606CCB bed narrowPeak optimal idr thresholded peaks ENCSR620VIC ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-CEBPG-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF014ZNK, ENCFF593QEG, ENCFF851RZA 580428 ENCODE Processing Pipeline 36b3049693b2c5d3cc2c9991f4dbc99a https://www.encodeproject.org/files/ENCFF606CCB/@@download/ENCFF606CCB.bed.gz hg19 released borderline replicate concordance, missing genetic modification characterization ENCFF267FXT bed narrowPeak optimal idr thresholded peaks ENCSR382WLL ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ELK1-human DNA False 2016-02-16 ENCODE 1, 3 ENCFF001TDO, ENCFF789XUC, ENCFF856LKK, ENCFF927LSX 149657 ENCODE Processing Pipeline 79a57420a683f66d501e513cb37dfda0 https://www.encodeproject.org/files/ENCFF267FXT/@@download/ENCFF267FXT.bed.gz hg19 released borderline replicate concordance duplicate lane review ENCFF617CAZ bed narrowPeak optimal idr thresholded peaks ENCSR047LSJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens TAF15-human DNA SDS formaldehyde False 2017-02-27 ENCODE 1, 2 ENCFF001TDO, ENCFF151HYU, ENCFF690XXK, ENCFF789HHG 14792 ENCODE Processing Pipeline 454b3aaf30cc5d814dc031bb5e8ca333 https://www.encodeproject.org/files/ENCFF617CAZ/@@download/ENCFF617CAZ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity ENCFF002CTQ bed narrowPeak optimal idr thresholded peaks ENCSR000EVG ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZNF274-human DNA see document see document False 2011-10-29 ENCODE 2349 ENCODE Consortium Analysis Working Group e6be10ccea019d58d0316cc3e758334e https://www.encodeproject.org/files/ENCFF002CTQ/@@download/ENCFF002CTQ.bed.gz hg19 released low read length, inconsistent platforms, mixed read lengths missing derived_from, biological replicates with identical biosample insufficient read length ENCFF973OME bed narrowPeak optimal idr thresholded peaks ENCSR979QYJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens MNT-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF215LBC, ENCFF513RYM, ENCFF671OVE 404380 ENCODE Processing Pipeline 19ef8e287c2b6736403247c2b5842fef https://www.encodeproject.org/files/ENCFF973OME/@@download/ENCFF973OME.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF456YII bed narrowPeak optimal idr thresholded peaks ENCSR828NCB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens GATAD2B-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF040LOQ, ENCFF271HBJ, ENCFF855RKW 635087 ENCODE Processing Pipeline d393dfe420253ec3d9141425df3f5a5b https://www.encodeproject.org/files/ENCFF456YII/@@download/ENCFF456YII.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF349MPF bed narrowPeak optimal idr thresholded peaks ENCSR509FWH ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens DPF2-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF150YMV, ENCFF496AHM, ENCFF943NIH 812699 ENCODE Processing Pipeline 811b29846fc1fc213785d04af598d88f https://www.encodeproject.org/files/ENCFF349MPF/@@download/ENCFF349MPF.bed.gz hg19 released mild to moderate bottlenecking ENCFF721LDD bed narrowPeak optimal idr thresholded peaks ENCSR011PEI ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ZNF175-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF195EMK, ENCFF260RNL, ENCFF472SCD 349948 ENCODE Processing Pipeline ce3af08120a96fe3dd29ae6b4b209bae https://www.encodeproject.org/files/ENCFF721LDD/@@download/ENCFF721LDD.bed.gz hg19 released control low read depth, mild to moderate bottlenecking, low read depth, missing genetic modification characterization ENCFF287NXV bed narrowPeak optimal idr thresholded peaks ENCSR894QWM ChIP-seq EFO:0005724 MM.1S cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF370UMM, ENCFF865JLD, ENCFF989VGU 18478 ENCODE Processing Pipeline d102157a37eff9c1a140a40c66dfb87e https://www.encodeproject.org/files/ENCFF287NXV/@@download/ENCFF287NXV.bed.gz hg19 released low read length, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF386TTQ bed narrowPeak optimal idr thresholded peaks ENCSR502NRF ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ELF1-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF138HSD, ENCFF491EBX, ENCFF938JGP 383450 ENCODE Processing Pipeline 9d08e04428458646839522bdc4265354 https://www.encodeproject.org/files/ENCFF386TTQ/@@download/ENCFF386TTQ.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF462JFW bed narrowPeak optimal idr thresholded peaks ENCSR706BJO ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ZBTB11-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF162YHD, ENCFF847LNA, ENCFF999XQG 421045 ENCODE Processing Pipeline cbf4d9f37773b9077321587efc291d1d https://www.encodeproject.org/files/ENCFF462JFW/@@download/ENCFF462JFW.bed.gz hg19 released missing genetic modification characterization ENCFF478KCU bed narrowPeak optimal idr thresholded peaks ENCSR096KPA ChIP-seq EFO:0005723 GM23248 cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-03-04 ENCODE 1, 2 ENCFF001TDO, ENCFF253NDQ, ENCFF311GKF, ENCFF980FHO 168481 ENCODE Processing Pipeline ca933600ea2d3517a032cb0412782c3e https://www.encodeproject.org/files/ENCFF478KCU/@@download/ENCFF478KCU.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO insufficient read depth ENCFF584YYH bed narrowPeak optimal idr thresholded peaks ENCSR000EEG ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RAD21-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF550URY, ENCFF741VOR, ENCFF770CIC 705911 ENCODE Processing Pipeline a82ee2006f39ecbc61fc9f369c4f5341 https://www.encodeproject.org/files/ENCFF584YYH/@@download/ENCFF584YYH.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF880SXP bed narrowPeak optimal idr thresholded peaks ENCSR278JQG ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens IKZF1-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF727PSQ, ENCFF835OWQ, ENCFF916ARR 47660 ENCODE Processing Pipeline 5b7572ab56cf4c0cce401f0880eb3529 https://www.encodeproject.org/files/ENCFF880SXP/@@download/ENCFF880SXP.bed.gz hg19 released borderline replicate concordance ENCFF473RXY bed narrowPeak optimal idr thresholded peaks ENCSR000DRZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF303UAB, ENCFF559IXF, ENCFF918HTJ 645089 ENCODE Processing Pipeline 9263eb7386faf2870ea728ae87b40a30 https://www.encodeproject.org/files/ENCFF473RXY/@@download/ENCFF473RXY.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth extremely low read depth ENCFF231VAA bed narrowPeak optimal idr thresholded peaks ENCSR389BLX ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GATAD2B-human DNA False 2016-10-26 ENCODE 1, 2 ENCFF001TDO, ENCFF195SFI, ENCFF697TMT, ENCFF938OWG 56375 ENCODE Processing Pipeline 88eb6873f70ac1b132216ad014effc17 https://www.encodeproject.org/files/ENCFF231VAA/@@download/ENCFF231VAA.bed.gz hg19 released ENCFF549TYR bed narrowPeak optimal idr thresholded peaks ENCSR000EGE ChIP-seq EFO:0002067 K562 cell line Homo sapiens EP300-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF140XPK, ENCFF379CMJ, ENCFF721DKV 499007 ENCODE Processing Pipeline 5c12903e8565056220d8fa3f42c54529 https://www.encodeproject.org/files/ENCFF549TYR/@@download/ENCFF549TYR.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF966MVC bed narrowPeak optimal idr thresholded peaks ENCSR412CTM ChIP-seq EFO:0002067 K562 cell line Homo sapiens SUZ12-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF009PGQ, ENCFF107SGI, ENCFF341WWD 45116 ENCODE Processing Pipeline 1567fb3dc23551e8036656e989bcb56f https://www.encodeproject.org/files/ENCFF966MVC/@@download/ENCFF966MVC.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance ENCFF333UCS bed narrowPeak optimal idr thresholded peaks ENCSR240XWM ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens LEF1-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF028UBX, ENCFF072ERX, ENCFF461RDS 67533 ENCODE Processing Pipeline 9c024f81116a4662a6b618d79c6b16c0 https://www.encodeproject.org/files/ENCFF333UCS/@@download/ENCFF333UCS.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF518OUJ bed narrowPeak optimal idr thresholded peaks ENCSR591EBL ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NBN-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF231ULR, ENCFF736SWB, ENCFF934HUV 58866 ENCODE Processing Pipeline 6168710fa83a5c083f8133657ff846a4 https://www.encodeproject.org/files/ENCFF518OUJ/@@download/ENCFF518OUJ.bed.gz hg19 released file validation error mismatched file status ENCFF763AAE bed narrowPeak optimal idr thresholded peaks ENCSR522LDJ ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens HDGF-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF325LIS, ENCFF420XDI, ENCFF948KJG 62705 ENCODE Processing Pipeline ec725059665594e94aa84a79c6e18af9 https://www.encodeproject.org/files/ENCFF763AAE/@@download/ENCFF763AAE.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF298VCE bed narrowPeak optimal idr thresholded peaks ENCSR555PBN ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MAFK-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF057RCM, ENCFF215LEX, ENCFF915SCX 229725 ENCODE Processing Pipeline a49314d3746a847846deb7ec319b9564 https://www.encodeproject.org/files/ENCFF298VCE/@@download/ENCFF298VCE.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity experiment not submitted to GEO partially characterized antibody ENCFF053TBK bed narrowPeak optimal idr thresholded peaks ENCSR064LJN ChIP-seq EFO:0001086 A549 cell line Homo sapiens RFX5-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF417FAK, ENCFF678TZR, ENCFF844VMC 118243 ENCODE Processing Pipeline e22a0a18cb43373f975e5942d390db9b https://www.encodeproject.org/files/ENCFF053TBK/@@download/ENCFF053TBK.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF556DEP bed narrowPeak optimal idr thresholded peaks ENCSR683CSF ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF207-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF369GTZ, ENCFF459AGI, ENCFF694FNL 26931 ENCODE Processing Pipeline c521f53794c533f3c0ed06c7b4434069 https://www.encodeproject.org/files/ENCFF556DEP/@@download/ENCFF556DEP.bed.gz hg19 released antibody characterized with exemption ENCFF637SBD bed narrowPeak optimal idr thresholded peaks ENCSR103GAK ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-ZNF175-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF035JZF, ENCFF126KMD, ENCFF567MYL 18038 ENCODE Processing Pipeline 666bc52045a14237131db8a8e0a1b7fc https://www.encodeproject.org/files/ENCFF637SBD/@@download/ENCFF637SBD.bed.gz hg19 released borderline replicate concordance, missing genetic modification characterization missing control alignments ENCFF229YSW bed narrowPeak optimal idr thresholded peaks ENCSR874AFU ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens IKZF1-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF455HXY, ENCFF492EAL, ENCFF795PEX 1279497 ENCODE Processing Pipeline 82175322dd3d0a9e2c11ada5394bf2a7 https://www.encodeproject.org/files/ENCFF229YSW/@@download/ENCFF229YSW.bed.gz hg19 released mild to moderate bottlenecking ENCFF895QLA bed narrowPeak optimal idr thresholded peaks ENCSR137ZMQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens REST-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF116JZW, ENCFF267RGU, ENCFF876EHZ 767264 ENCODE Processing Pipeline 566a637ff871d08a8eb27aa1153826fb https://www.encodeproject.org/files/ENCFF895QLA/@@download/ENCFF895QLA.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF658YLW bed narrowPeak optimal idr thresholded peaks ENCSR545FXC ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ATF7-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF302KGG, ENCFF556TCV, ENCFF684VZS 712827 ENCODE Processing Pipeline e36045cc8769b117f494406dc120ea94 https://www.encodeproject.org/files/ENCFF658YLW/@@download/ENCFF658YLW.bed.gz hg19 released antibody characterized with exemption ENCFF998YJY bed narrowPeak optimal idr thresholded peaks ENCSR563LLO ChIP-seq EFO:0002067 K562 cell line Homo sapiens E2F1-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF159RHZ, ENCFF218RJK, ENCFF710KKZ 145663 ENCODE Processing Pipeline 167456f68af8d185c73af8324361f14e https://www.encodeproject.org/files/ENCFF998YJY/@@download/ENCFF998YJY.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF785ZQF bed narrowPeak optimal idr thresholded peaks ENCSR636EYA ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTBP1-human DNA False 2016-04-21 ENCODE 1, 2 ENCFF001TDO, ENCFF890VHF, ENCFF922CFN, ENCFF941VDL 592985 ENCODE Processing Pipeline 643de89c03671376dce833c8c354adf7 https://www.encodeproject.org/files/ENCFF785ZQF/@@download/ENCFF785ZQF.bed.gz hg19 released ENCFF588OLK bed narrowPeak optimal idr thresholded peaks ENCSR780BBJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZZZ3-human DNA False 2016-12-05 ENCODE 1, 2 ENCFF001TDO, ENCFF433ANO, ENCFF639RPL, ENCFF975UYT 59489 ENCODE Processing Pipeline 21ad5e41efc93bdc0af0f6d786d80664 https://www.encodeproject.org/files/ENCFF588OLK/@@download/ENCFF588OLK.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity, antibody characterized with exemption ENCFF237UAN bed narrowPeak optimal idr thresholded peaks ENCSR041AXL ChIP-seq EFO:0002067 K562 cell line Homo sapiens RFX1-human DNA False 2016-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF008XTO, ENCFF811RGP, ENCFF830YCS 297362 ENCODE Processing Pipeline cf2d85601c8811ad39574a73908395c8 https://www.encodeproject.org/files/ENCFF237UAN/@@download/ENCFF237UAN.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF966RPL bed narrowPeak optimal idr thresholded peaks ENCSR293QAR ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MTA2-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF407KWG, ENCFF494SRY, ENCFF593KRH 789765 ENCODE Processing Pipeline 44b35b24f90013b12bb762c2c84bd65c https://www.encodeproject.org/files/ENCFF966RPL/@@download/ENCFF966RPL.bed.gz hg19 released file validation error, mild to moderate bottlenecking, low read depth, moderate library complexity mismatched file status ENCFF012JXJ bed narrowPeak optimal idr thresholded peaks ENCSR636MKU ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BACH1-human DNA False 2017-01-31 ENCODE 3, 4 ENCFF001TDO, ENCFF084PVB, ENCFF747JGV, ENCFF866OLZ 440429 ENCODE Processing Pipeline 444df22c98d4fcff23ed0065c0dcd22e https://www.encodeproject.org/files/ENCFF012JXJ/@@download/ENCFF012JXJ.bed.gz hg19 released mild to moderate bottlenecking ENCFF743FZS bed narrowPeak optimal idr thresholded peaks ENCSR384LYW ChIP-seq CL:0000182 hepatocyte in vitro differentiated cells Homo sapiens EZH2-human DNA False 2016-11-23 ENCODE 1, 2 ENCFF001TDO, ENCFF367LDH, ENCFF482XGS, ENCFF557NXL 211111 ENCODE Processing Pipeline 08a0432a038c13d0b4ea21714a84fb36 https://www.encodeproject.org/files/ENCFF743FZS/@@download/ENCFF743FZS.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, antibody characterized with exemption NTR biosample ENCFF199GND bed narrowPeak optimal idr thresholded peaks ENCSR923UTX ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NONO-human DNA SDS formaldehyde False 2017-08-17 ENCODE 1, 2 ENCFF001TDO, ENCFF170DYF, ENCFF246YPT, ENCFF572LJS 362880 ENCODE Processing Pipeline ad6ac579bcd3ac2285eef43ba5157ecc https://www.encodeproject.org/files/ENCFF199GND/@@download/ENCFF199GND.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF817QHW bed narrowPeak optimal idr thresholded peaks ENCSR332EYT ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens STAT1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF073OWF, ENCFF709QKK, ENCFF921NFP 189647 ENCODE Processing Pipeline e19074d05cfeb97f1ebf25e868bd35da https://www.encodeproject.org/files/ENCFF817QHW/@@download/ENCFF817QHW.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, antibody characterized with exemption ENCFF807AKG bed narrowPeak optimal idr thresholded peaks ENCSR841NDX ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ELF1-human DNA False 2017-06-26 ENCODE 1, 2 ENCFF001TDO, ENCFF244PNH, ENCFF359FUJ, ENCFF756XID 584709 ENCODE Processing Pipeline c254faee11bb0ce333fb9396a04593c5 https://www.encodeproject.org/files/ENCFF807AKG/@@download/ENCFF807AKG.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF785FBD bed narrowPeak optimal idr thresholded peaks ENCSR789GVU ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens BHLHE40-human DNA False 2016-11-18 ENCODE 1, 2 ENCFF001TDO, ENCFF207ZRW, ENCFF562GBY, ENCFF649FUD 20912 ENCODE Processing Pipeline 000680229ad85adad7aba34745d43dd7 https://www.encodeproject.org/files/ENCFF785FBD/@@download/ENCFF785FBD.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity duplicate lane review ENCFF530LSA bed narrowPeak optimal idr thresholded peaks ENCSR145CXH ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TARDBP-human DNA SDS formaldehyde False 2017-12-01 ENCODE 1, 2 ENCFF001TDO, ENCFF625LUF, ENCFF640MOW, ENCFF657QUD 131195 ENCODE Processing Pipeline 4a92466ac0c7aa892d275f40b241a09e https://www.encodeproject.org/files/ENCFF530LSA/@@download/ENCFF530LSA.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance experiment not submitted to GEO ENCFF836HHL bed narrowPeak optimal idr thresholded peaks ENCSR062HDL ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens HSF1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF232NKH, ENCFF569FCI, ENCFF663REE 48324 ENCODE Processing Pipeline 8eea9b37a3808a81eaacdcb2652d7c12 https://www.encodeproject.org/files/ENCFF836HHL/@@download/ENCFF836HHL.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF324TBP bed narrowPeak optimal idr thresholded peaks ENCSR101FJU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF384-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF037XHM, ENCFF147SMY, ENCFF313BLC 281422 ENCODE Processing Pipeline 5c67758efa36fc46a013b34d27c7fd43 https://www.encodeproject.org/files/ENCFF324TBP/@@download/ENCFF324TBP.bed.gz hg19 released low read length ENCFF795QZU bed narrowPeak optimal idr thresholded peaks ENCSR841YWU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens E4F1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF329QXP, ENCFF636VMF, ENCFF995GUT 66521 ENCODE Processing Pipeline 6f363b188c51b1846c21a87ed1df5d8f https://www.encodeproject.org/files/ENCFF795QZU/@@download/ENCFF795QZU.bed.gz hg19 released experiment not submitted to GEO partially characterized antibody ENCFF374BNP bed narrowPeak optimal idr thresholded peaks ENCSR785YRL ChIP-seq CL:0000775 neutrophil primary cell Homo sapiens CTCF-human DNA False 2016-12-01 ENCODE 1, 2 ENCFF001TDO, ENCFF070WIW, ENCFF536TDH, ENCFF736LBL 454345 ENCODE Processing Pipeline 683ef5fc6a8f9999e64a515baa290711 https://www.encodeproject.org/files/ENCFF374BNP/@@download/ENCFF374BNP.bed.gz hg19 released antibody characterized with exemption NTR biosample ENCFF175IIE bed narrowPeak optimal idr thresholded peaks ENCSR970NKQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR2F1-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF035WWJ, ENCFF224GWU, ENCFF359OAZ 603194 ENCODE Processing Pipeline adbe9db9e3821e3e5d266adc496d2cf0 https://www.encodeproject.org/files/ENCFF175IIE/@@download/ENCFF175IIE.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF808UCP bed narrowPeak optimal idr thresholded peaks ENCSR793USK ChIP-seq EFO:0002847 PC-9 cell line Homo sapiens EZH2-human DNA False 2017-11-13 ENCODE 1, 2 ENCFF001TDO, ENCFF258LFF, ENCFF656XHS, ENCFF819BDT 56008 ENCODE Processing Pipeline 4d3ef79bacb47f74d1904f3c34d3db11 https://www.encodeproject.org/files/ENCFF808UCP/@@download/ENCFF808UCP.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption experiment not submitted to GEO ENCFF502KHR bed narrowPeak optimal idr thresholded peaks ENCSR638QHV ChIP-seq EFO:0002067 K562 cell line Homo sapiens ELF4-human DNA False 2017-01-31 ENCODE 1, 2 ENCFF001TDO, ENCFF307JUJ, ENCFF625PVR, ENCFF734SUP 329872 ENCODE Processing Pipeline c2e187f6d861df3100e2acf5d12e3e45 https://www.encodeproject.org/files/ENCFF502KHR/@@download/ENCFF502KHR.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption ENCFF812MZB bed narrowPeak optimal idr thresholded peaks ENCSR234VCE ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens DPF2-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF193LNB, ENCFF546YTN, ENCFF557POD 401448 ENCODE Processing Pipeline 49e790bfe0c4b66b44837cc08eccf03d https://www.encodeproject.org/files/ENCFF812MZB/@@download/ENCFF812MZB.bed.gz hg19 released ENCFF314KRZ bed narrowPeak optimal idr thresholded peaks ENCSR176EXN ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens JUN-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF344TGN, ENCFF595WOT, ENCFF960PAB 119623 ENCODE Processing Pipeline 6792d61b88b8800d7d60aa74859ea231 https://www.encodeproject.org/files/ENCFF314KRZ/@@download/ENCFF314KRZ.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption ENCFF004WYV bed narrowPeak optimal idr thresholded peaks ENCSR211LTF ChIP-seq EFO:0002067 K562 cell line Homo sapiens EGR1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF343JJX, ENCFF634YJK, ENCFF920IJY 557721 ENCODE Processing Pipeline f1a92ff86172ca7ec73d6ddfff66ecc4 https://www.encodeproject.org/files/ENCFF004WYV/@@download/ENCFF004WYV.bed.gz hg19 released low read depth ENCFF418DRY bed narrowPeak optimal idr thresholded peaks ENCSR294JWV ChIP-seq EFO:0001086 A549 cell line Homo sapiens ZFP36-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF548GLK, ENCFF589LXR, ENCFF848NAZ 207120 ENCODE Processing Pipeline 4e93c7b4d77e37b74325e30f059ada18 https://www.encodeproject.org/files/ENCFF418DRY/@@download/ENCFF418DRY.bed.gz hg19 released borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF048JWL bed narrowPeak optimal idr thresholded peaks ENCSR934NHU ChIP-seq CL:0002319 neural cell in vitro differentiated cells Homo sapiens MXI1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF291JHS, ENCFF768FVV, ENCFF958NNA 549464 ENCODE Processing Pipeline b823de521ef5907f68bb2f6df358a678 https://www.encodeproject.org/files/ENCFF048JWL/@@download/ENCFF048JWL.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF193MKL bed narrowPeak optimal idr thresholded peaks ENCSR729LGA ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens SP1-human DNA False 2016-09-01 ENCODE 1, 2 ENCFF001TDO, ENCFF096VAL, ENCFF546ASI, ENCFF852HEY 54123 ENCODE Processing Pipeline cd90f0a39db101f4a65917b0ac20bf94 https://www.encodeproject.org/files/ENCFF193MKL/@@download/ENCFF193MKL.bed.gz hg19 released ENCFF189TVG bed narrowPeak optimal idr thresholded peaks ENCSR345YWJ ChIP-seq UBERON:0002107 liver tissue Homo sapiens ZBTB33-human DNA False 2016-09-23 ENCODE 1, 2 ENCFF001TDO, ENCFF426TDF, ENCFF719LYG, ENCFF873YWK 90623 ENCODE Processing Pipeline 9dea3ec7f9807e5c95f5d056631de6be https://www.encodeproject.org/files/ENCFF189TVG/@@download/ENCFF189TVG.bed.gz hg19 released borderline replicate concordance, low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF507RHE bed narrowPeak optimal idr thresholded peaks ENCSR928API ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RFX1-human DNA False 2017-11-14 ENCODE 2, 3 ENCFF001TDO, ENCFF458YFL, ENCFF523TOV, ENCFF905UQM 117007 ENCODE Processing Pipeline 645691ce6019368a11effa03e652dbb9 https://www.encodeproject.org/files/ENCFF507RHE/@@download/ENCFF507RHE.bed.gz hg19 released experiment not submitted to GEO ENCFF947IJX bed narrowPeak optimal idr thresholded peaks ENCSR611JJS ChIP-seq EFO:0002106 A673 cell line Homo sapiens CTCF-human DNA False 2017-11-13 ENCODE 1, 2 ENCFF001TDO, ENCFF317YVO, ENCFF455ZJN, ENCFF799ZCH 1016359 ENCODE Processing Pipeline 33ffb92f35aa7e03fa914fe0ba386406 https://www.encodeproject.org/files/ENCFF947IJX/@@download/ENCFF947IJX.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF827MDC bed narrowPeak optimal idr thresholded peaks ENCSR277OOQ ChIP-seq EFO:0001086 A549 cell line Homo sapiens ZC3H11A-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF087DBS, ENCFF088LGL, ENCFF279PWU 140359 ENCODE Processing Pipeline ace047c77db01927a4f200d44940abe0 https://www.encodeproject.org/files/ENCFF827MDC/@@download/ENCFF827MDC.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF968KBN bed narrowPeak optimal idr thresholded peaks ENCSR869IUD ChIP-seq EFO:0002067 K562 cell line Homo sapiens ATF2-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF513RYS, ENCFF759MWN, ENCFF826QEY 723708 ENCODE Processing Pipeline 4aad24f6ab0ecc423ff32a4a1989e087 https://www.encodeproject.org/files/ENCFF968KBN/@@download/ENCFF968KBN.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF246HIM bed narrowPeak optimal idr thresholded peaks ENCSR198ZYJ ChIP-seq CL:0002319 neural cell in vitro differentiated cells Homo sapiens RAD21-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF406ZDS, ENCFF567WYM, ENCFF830CSU 831522 ENCODE Processing Pipeline 7be299ee1f00b328b82605fa5e21fa6b https://www.encodeproject.org/files/ENCFF246HIM/@@download/ENCFF246HIM.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF809YFY bed narrowPeak optimal idr thresholded peaks ENCSR819LHG ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOXA1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF113ZZY, ENCFF837QWL, ENCFF996FCB 26422 ENCODE Processing Pipeline 853ae621eda61d33788aa4e3acaa8aba https://www.encodeproject.org/files/ENCFF809YFY/@@download/ENCFF809YFY.bed.gz hg19 released mild to moderate bottlenecking ENCFF099NBE bed narrowPeak optimal idr thresholded peaks ENCSR125DKL ChIP-seq EFO:0002357 SU-DHL-6 cell line Homo sapiens CTCF-human DNA see document see document False 2017-11-29 ENCODE 1, 2 ENCFF001TDO, ENCFF206YWO, ENCFF708ZIZ, ENCFF967NOV 1308100 ENCODE Processing Pipeline a0c9fc2538edaf3c7e6d716df6894959 https://www.encodeproject.org/files/ENCFF099NBE/@@download/ENCFF099NBE.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO insufficient read depth, poor library complexity, severe bottlenecking ENCFF341HWZ bed narrowPeak optimal idr thresholded peaks ENCSR408JQO ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens IRF3-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF294PGV, ENCFF527ONY, ENCFF942POQ 94616 ENCODE Processing Pipeline c59b54537720fe013b61c273bcdb7db5 https://www.encodeproject.org/files/ENCFF341HWZ/@@download/ENCFF341HWZ.bed.gz hg19 released mild to moderate bottlenecking ENCFF694UJI bed narrowPeak optimal idr thresholded peaks ENCSR219NRT ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens GTF2F1-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF266NSN, ENCFF401ZKP, ENCFF808UFI 48543 ENCODE Processing Pipeline 8c61a3021ba1648497bcc6c7e1a1d4d7 https://www.encodeproject.org/files/ENCFF694UJI/@@download/ENCFF694UJI.bed.gz hg19 released low read length, low read depth ENCFF696KPD bed narrowPeak optimal idr thresholded peaks ENCSR000BRR ChIP-seq EFO:0002067 K562 cell line Homo sapiens STAT5A-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF373WLW, ENCFF556KAN, ENCFF562UJV 241687 ENCODE Processing Pipeline c7fe8f342e3192db1d65922e864f8c7e https://www.encodeproject.org/files/ENCFF696KPD/@@download/ENCFF696KPD.bed.gz hg19 released low read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF471ZTZ bed narrowPeak optimal idr thresholded peaks ENCSR613NUC ChIP-seq EFO:0002067 K562 cell line Homo sapiens ARNT-human DNA False 2016-12-19 ENCODE 1, 2 ENCFF001TDO, ENCFF505URD, ENCFF829KFC, ENCFF848FSH 309156 ENCODE Processing Pipeline 720a3ea4fe1bb47e81c212a2969a67f6 https://www.encodeproject.org/files/ENCFF471ZTZ/@@download/ENCFF471ZTZ.bed.gz hg19 released ENCFF662IOC bed narrowPeak optimal idr thresholded peaks ENCSR430YRJ ChIP-seq EFO:0005694 KMS-11 cell line Homo sapiens CTCF-human DNA False 2017-11-13 ENCODE 1, 2 ENCFF001TDO, ENCFF578FSD, ENCFF595GMF, ENCFF850KMN 889131 ENCODE Processing Pipeline 88ccf4f9fadb93f1bcfff9069c661557 https://www.encodeproject.org/files/ENCFF662IOC/@@download/ENCFF662IOC.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF421PBO bed narrowPeak optimal idr thresholded peaks ENCSR084RDK ChIP-seq EFO:0002167 DOHH2 cell line Homo sapiens CTCF-human DNA see document see document False 2014-07-11 ENCODE 1, 2 ENCFF001TDO, ENCFF268CZL, ENCFF459CAS, ENCFF824YYD 1053984 ENCODE Processing Pipeline d43f7f5ed061c81af73fc2007fc4995e https://www.encodeproject.org/files/ENCFF421PBO/@@download/ENCFF421PBO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption NTR biosample poor library complexity, severe bottlenecking ENCFF975IRM bed narrowPeak optimal idr thresholded peaks ENCSR670JDQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens RB1-human DNA False 2017-03-16 ENCODE 3, 4 ENCFF001TDO, ENCFF197MJO, ENCFF634SVO, ENCFF801LNJ 469880 ENCODE Processing Pipeline 36677304d38b5f80815daf0f71286681 https://www.encodeproject.org/files/ENCFF975IRM/@@download/ENCFF975IRM.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF942FBW bed narrowPeak optimal idr thresholded peaks ENCSR957KYB ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens BHLHE40-human DNA False 2016-09-01 ENCODE 1, 2 ENCFF001TDO, ENCFF088IEB, ENCFF619TUA, ENCFF940YUU 463177 ENCODE Processing Pipeline e4cca3a1db075fe4246889df1b37db5f https://www.encodeproject.org/files/ENCFF942FBW/@@download/ENCFF942FBW.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth duplicate lane review ENCFF823SYE bed narrowPeak optimal idr thresholded peaks ENCSR715CCR ChIP-seq EFO:0002067 K562 cell line Homo sapiens DPF2-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF023VOJ, ENCFF577FLU, ENCFF994IZJ 812173 ENCODE Processing Pipeline 59b72560947ff818b0d51aac88596a9b https://www.encodeproject.org/files/ENCFF823SYE/@@download/ENCFF823SYE.bed.gz hg19 released ENCFF297BXM bed narrowPeak optimal idr thresholded peaks ENCSR488EES ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NFE2L2-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF126HBJ, ENCFF144BHZ, ENCFF596MOA 170579 ENCODE Processing Pipeline bee2941bec91c7c87a5e2348f00cbff5 https://www.encodeproject.org/files/ENCFF297BXM/@@download/ENCFF297BXM.bed.gz hg19 released low read length ENCFF357WYN bed narrowPeak optimal idr thresholded peaks ENCSR189YYK ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZBTB40-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF297SZY, ENCFF321DBH, ENCFF742SNU 335989 ENCODE Processing Pipeline 2daa2dcb35564976ae966e9a8f326dce https://www.encodeproject.org/files/ENCFF357WYN/@@download/ENCFF357WYN.bed.gz hg19 released file validation error, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity mismatched file status ENCFF906IMT bed narrowPeak optimal idr thresholded peaks ENCSR382XLA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZFP36-human DNA False 2018-01-26 ENCODE 2, 3 ENCFF001TDO, ENCFF722ERB, ENCFF806XIE, ENCFF844TSM 61616 ENCODE Processing Pipeline 9b285ff6f7a58bdc0f47d6bbb2e49475 https://www.encodeproject.org/files/ENCFF906IMT/@@download/ENCFF906IMT.bed.gz hg19 released low read length, borderline replicate concordance, low read depth experiment not submitted to GEO partially characterized antibody ENCFF125YHG bed narrowPeak optimal idr thresholded peaks ENCSR481YWD ChIP-seq EFO:0001086 A549 cell line Homo sapiens SMC3-human DNA False 2016-10-31 ENCODE 1, 2 ENCFF001TDO, ENCFF371DJF, ENCFF787LTE, ENCFF953EDE 351597 ENCODE Processing Pipeline 912d123a1abc3ca45eb6c1e41fea7608 https://www.encodeproject.org/files/ENCFF125YHG/@@download/ENCFF125YHG.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF300XUA bed narrowPeak optimal idr thresholded peaks ENCSR991ELG ChIP-seq EFO:0002067 K562 cell line Homo sapiens SP1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF103ESU, ENCFF269OJD, ENCFF778OYJ 267916 ENCODE Processing Pipeline 375188392fd2e30179eec9249863ee49 https://www.encodeproject.org/files/ENCFF300XUA/@@download/ENCFF300XUA.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF572YVL bed narrowPeak optimal idr thresholded peaks ENCSR017CEO ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CUX1-human DNA False 2016-06-14 ENCODE 2, 3 ENCFF001TDO, ENCFF411WAC, ENCFF508BAI, ENCFF876DVV 310550 ENCODE Processing Pipeline f198a4bd13b4f6eea757257bd24eb6e7 https://www.encodeproject.org/files/ENCFF572YVL/@@download/ENCFF572YVL.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF002CVC bed narrowPeak optimal idr thresholded peaks ENCSR000EFA ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens JUN-human DNA see document see document False 2011-10-29 ENCODE 682671 ENCODE Consortium Analysis Working Group 633e29aea0b8daae7a7633161281b118 https://www.encodeproject.org/files/ENCFF002CVC/@@download/ENCFF002CVC.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF072ZEU bed narrowPeak optimal idr thresholded peaks ENCSR125NBL ChIP-seq NTR:0000711 neural progenitor cell in vitro differentiated cells Homo sapiens CTCF-human DNA False 2017-10-19 ENCODE 1, 2 ENCFF001TDO, ENCFF230HEO, ENCFF888EDU, ENCFF983BJS 1051859 ENCODE Processing Pipeline 1aeb7830409a87e0443bd93fbd773235 https://www.encodeproject.org/files/ENCFF072ZEU/@@download/ENCFF072ZEU.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF905EBM bed narrowPeak optimal idr thresholded peaks ENCSR703KWN ChIP-seq EFO:0005724 MM.1S cell line Homo sapiens EZH2-human DNA False 2017-12-14 ENCODE 1, 2 ENCFF001TDO, ENCFF138QJZ, ENCFF355WZV, ENCFF725JDK 27025 ENCODE Processing Pipeline 6f8fb897b7d3c2a99b4b4753454bc67f https://www.encodeproject.org/files/ENCFF905EBM/@@download/ENCFF905EBM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption, mixed read lengths experiment not submitted to GEO ENCFF911RQN bed narrowPeak optimal idr thresholded peaks ENCSR753GIA ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens TARDBP-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF278ZIL, ENCFF397APL, ENCFF614ENJ 60947 ENCODE Processing Pipeline 057cbd7bec7f84d0b6e7978a79558d2e https://www.encodeproject.org/files/ENCFF911RQN/@@download/ENCFF911RQN.bed.gz hg19 released ENCFF883EGI bed narrowPeak optimal idr thresholded peaks ENCSR000BQF ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens TAF1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF363MZC, ENCFF534OBN, ENCFF893LMP 296975 ENCODE Processing Pipeline a0c63d69cf64140819bd535ff869d781 https://www.encodeproject.org/files/ENCFF883EGI/@@download/ENCFF883EGI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample ENCFF965AIZ bed narrowPeak optimal idr thresholded peaks ENCSR569XNP ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens FOS-human DNA False 2016-12-19 ENCODE 1, 3 ENCFF001TDO, ENCFF124QJZ, ENCFF540SXF, ENCFF834BCC 1138063 ENCODE Processing Pipeline 23514fe2f2689d4cb62e6fe4fc279273 https://www.encodeproject.org/files/ENCFF965AIZ/@@download/ENCFF965AIZ.bed.gz hg19 released duplicate lane review ENCFF582SHF bed narrowPeak optimal idr thresholded peaks ENCSR404BPV ChIP-seq CL:0002319 neural cell in vitro differentiated cells Homo sapiens SMC3-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF040TAT, ENCFF067FOD, ENCFF975MKK 902257 ENCODE Processing Pipeline 1913e84f8d444712f5c7cb57f2ee697a https://www.encodeproject.org/files/ENCFF582SHF/@@download/ENCFF582SHF.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption experiment not submitted to GEO poor library complexity ENCFF088WYS bed narrowPeak optimal idr thresholded peaks ENCSR000BSA ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens JUND-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF215YYW, ENCFF383XWW, ENCFF772HIT 429111 ENCODE Processing Pipeline 552adbf4f3cb71bf7ca90692e963e8df https://www.encodeproject.org/files/ENCFF088WYS/@@download/ENCFF088WYS.bed.gz hg19 released low read depth biological replicates with identical biosample missing control alignments ENCFF545VNY bed narrowPeak optimal idr thresholded peaks ENCSR000FCE ChIP-seq EFO:0002067 K562 cell line Homo sapiens ETV6-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF235BMG, ENCFF539MNA, ENCFF915TWO 122108 ENCODE Processing Pipeline a29ad50d06ead7823ea05e7b4a848633 https://www.encodeproject.org/files/ENCFF545VNY/@@download/ENCFF545VNY.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF660VPM bed narrowPeak optimal idr thresholded peaks ENCSR124BJR ChIP-seq EFO:0002067 K562 cell line Homo sapiens ETV6-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF315GZR, ENCFF558BWS, ENCFF611XPF 48570 ENCODE Processing Pipeline 627872c6c63dc5283d8687e9efa8fe7b https://www.encodeproject.org/files/ENCFF660VPM/@@download/ENCFF660VPM.bed.gz hg19 released low read length, borderline replicate concordance, low read depth ENCFF675TLS bed narrowPeak optimal idr thresholded peaks ENCSR267DFA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXA1-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF400BJI, ENCFF432MIZ, ENCFF549YDX 167811 ENCODE Processing Pipeline 34278c629fe0428ac2f4c6dfa275bc15 https://www.encodeproject.org/files/ENCFF675TLS/@@download/ENCFF675TLS.bed.gz hg19 released ENCFF941ZLF bed narrowPeak optimal idr thresholded peaks ENCSR783QUL ChIP-seq EFO:0007112 Loucy cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF107IVH, ENCFF262SHR, ENCFF407UZQ 21974 ENCODE Processing Pipeline 8ab509e27ba0756df3d37fedaf0bc99d https://www.encodeproject.org/files/ENCFF941ZLF/@@download/ENCFF941ZLF.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF499OUD bed narrowPeak optimal idr thresholded peaks ENCSR000BRF ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour JUND-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF154EAD, ENCFF740MCA, ENCFF804HAX 358511 ENCODE Processing Pipeline 7009bdfb16748b7dc7f7f7d5c9b2d1ec https://www.encodeproject.org/files/ENCFF499OUD/@@download/ENCFF499OUD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF901BGG bed narrowPeak optimal idr thresholded peaks ENCSR673WZL ChIP-seq EFO:0002071 LNCAP cell line Homo sapiens 17β-hydroxy-5α-androstan-3-one 10 nM 4 hour CTCF-human DNA False 2017-06-29 ENCODE 1, 2 ENCFF001TDO, ENCFF265NZD, ENCFF499RVM, ENCFF696QFR 771337 ENCODE Processing Pipeline 7c52b039f0a5e21db97ef3f12a4d997b https://www.encodeproject.org/files/ENCFF901BGG/@@download/ENCFF901BGG.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF116DIO bed narrowPeak optimal idr thresholded peaks ENCSR018MSO ChIP-seq EFO:0002067 K562 cell line Homo sapiens eGFP-ZNF148-human DNA False 2017-12-01 ENCODE 3, 4 ENCFF001TDO, ENCFF297GYL, ENCFF890QZH, ENCFF985CUX 412739 ENCODE Processing Pipeline 1373edacc8e8c659850e64d69646692f https://www.encodeproject.org/files/ENCFF116DIO/@@download/ENCFF116DIO.bed.gz hg19 released missing genetic modification characterization experiment not submitted to GEO ENCFF002CSG bed narrowPeak optimal idr thresholded peaks ENCSR000EVJ ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens E2F1-human DNA see document see document False 2011-10-29 ENCODE 129469 ENCODE Consortium Analysis Working Group ef923581e8e46df0f60fbaf91c75ca6e https://www.encodeproject.org/files/ENCFF002CSG/@@download/ENCFF002CSG.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF581YKY bed narrowPeak optimal idr thresholded peaks ENCSR986CDX ChIP-seq EFO:0002067 K562 cell line Homo sapiens NEUROD1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF314SAN, ENCFF334IIE, ENCFF973JKQ 252531 ENCODE Processing Pipeline de1c71d16bed9d96dcff38981ba5dd30 https://www.encodeproject.org/files/ENCFF581YKY/@@download/ENCFF581YKY.bed.gz hg19 released low read length, borderline replicate concordance, low read depth experiment not submitted to GEO partially characterized antibody ENCFF640LEB bed narrowPeak optimal idr thresholded peaks ENCSR297MUV ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens EZH2phosphoT487-human DNA False 2017-01-15 ENCODE 1, 2 ENCFF001TDO, ENCFF139FDW, ENCFF252AKV, ENCFF978OGV 35158 ENCODE Processing Pipeline bd8c5e4680bcbbd808ba239c174fd1a6 https://www.encodeproject.org/files/ENCFF640LEB/@@download/ENCFF640LEB.bed.gz hg19 released borderline replicate concordance, moderate library complexity, mild to moderate bottlenecking, mixed run types, low read depth, antibody characterized with exemption NTR biosample ENCFF760IFZ bed narrowPeak optimal idr thresholded peaks ENCSR626VUC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ETV6-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF021LAP, ENCFF283QCO, ENCFF305DNA 370617 ENCODE Processing Pipeline fc6b1747ced34ffb5b0c695b5120610d https://www.encodeproject.org/files/ENCFF760IFZ/@@download/ENCFF760IFZ.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption mismatched file status ENCFF583CIY bed narrowPeak optimal idr thresholded peaks ENCSR494UQJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR3C1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF269CZZ, ENCFF923WYM, ENCFF939VKQ 73618 ENCODE Processing Pipeline fab8230df4fac667f59e49a65da4daab https://www.encodeproject.org/files/ENCFF583CIY/@@download/ENCFF583CIY.bed.gz hg19 released borderline replicate concordance, low read depth experiment not submitted to GEO partially characterized antibody ENCFF988IOQ bed narrowPeak optimal idr thresholded peaks ENCSR000DMF ChIP-seq EFO:0005726 LNCaP clone FGC cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF195CRO, ENCFF337SGV, ENCFF867DDR 835569 ENCODE Processing Pipeline 229b8bc3f4c57961455ee29ab67d5f55 https://www.encodeproject.org/files/ENCFF988IOQ/@@download/ENCFF988IOQ.bed.gz hg19 released mild to moderate bottlenecking biological replicates with identical biosample control insufficient read depth, insufficient read depth ENCFF147MAN bed narrowPeak optimal idr thresholded peaks ENCSR444LIN ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TCF7-human DNA False 2016-08-10 ENCODE 1, 2 ENCFF001TDO, ENCFF237AGN, ENCFF412SBF, ENCFF575WAL 334161 ENCODE Processing Pipeline 10b950f75ae36b7a32659dcdfc3bd99b https://www.encodeproject.org/files/ENCFF147MAN/@@download/ENCFF147MAN.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF150STV bed narrowPeak optimal idr thresholded peaks ENCSR000BIO ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF326RDQ, ENCFF734DHL, ENCFF978KSK 11618 ENCODE Processing Pipeline 2505f610e615fcc77e60f7bbc8ef9d14 https://www.encodeproject.org/files/ENCFF150STV/@@download/ENCFF150STV.bed.gz hg19 released control low read depth, low read length, low read depth biological replicates with identical biosample ENCFF615FIR bed narrowPeak optimal idr thresholded peaks ENCSR028NUR ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF592-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF096FDT, ENCFF134UIM, ENCFF185LGF 16924 ENCODE Processing Pipeline 87ab6ffc70c2d9d03c2b87caf8e4673b https://www.encodeproject.org/files/ENCFF615FIR/@@download/ENCFF615FIR.bed.gz hg19 released borderline replicate concordance, low read depth ENCFF318SDF bed narrowPeak optimal idr thresholded peaks ENCSR000BIQ ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens SIX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF493YRO, ENCFF883CRS, ENCFF946SYP 56542 ENCODE Processing Pipeline a99c9330c815a30deec33b4d13251ca2 https://www.encodeproject.org/files/ENCFF318SDF/@@download/ENCFF318SDF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample missing control alignments ENCFF315YAF bed narrowPeak optimal idr thresholded peaks ENCSR038DJJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens SMAD1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF067UPX, ENCFF328DUA, ENCFF567MRG 163107 ENCODE Processing Pipeline 00df6f6748c20e2ecc98bc3d078b2bd2 https://www.encodeproject.org/files/ENCFF315YAF/@@download/ENCFF315YAF.bed.gz hg19 released low read length, low read depth experiment not submitted to GEO partially characterized antibody ENCFF332PGQ bed narrowPeak optimal idr thresholded peaks ENCSR000BKA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ETS1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF075PCI, ENCFF570ZKC, ENCFF883DUG 223403 ENCODE Processing Pipeline e5bebc61c5e4cd79bae1c050a283c860 https://www.encodeproject.org/files/ENCFF332PGQ/@@download/ENCFF332PGQ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample ENCFF713IVN bed narrowPeak optimal idr thresholded peaks ENCSR000BIB ChIP-seq EFO:0002786 GM12892 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF365FTH, ENCFF452NTV, ENCFF556WPW 210518 ENCODE Processing Pipeline 69d8b7fd6e1831171aa71f7a143393a4 https://www.encodeproject.org/files/ENCFF713IVN/@@download/ENCFF713IVN.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF123WEZ bed narrowPeak optimal idr thresholded peaks ENCSR207PFI ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZBED1-human DNA False 2016-02-05 ENCODE 1, 2 ENCFF001TDO, ENCFF196ECC, ENCFF493ZGH, ENCFF846TRX 217520 ENCODE Processing Pipeline 6c56ef3935736be7731a0100ba97731f https://www.encodeproject.org/files/ENCFF123WEZ/@@download/ENCFF123WEZ.bed.gz hg19 released borderline replicate concordance ENCFF065EPE bed narrowPeak optimal idr thresholded peaks ENCSR000BJK ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens GABPA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF348PXE, ENCFF451PTD, ENCFF539SWX 145608 ENCODE Processing Pipeline fb8bebc60129799408d9866b62709e23 https://www.encodeproject.org/files/ENCFF065EPE/@@download/ENCFF065EPE.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF208AFB bed narrowPeak optimal idr thresholded peaks ENCSR000EDO ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CEBPZ-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF038ZOH, ENCFF884XPS, ENCFF929SGA 9470 ENCODE Processing Pipeline d920db9d39dce27b60ab03fd7bb65dad https://www.encodeproject.org/files/ENCFF208AFB/@@download/ENCFF208AFB.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF061UXU bed narrowPeak optimal idr thresholded peaks ENCSR088HZI ChIP-seq EFO:0002357 SU-DHL-6 cell line Homo sapiens EZH2phosphoT487-human DNA see document see document False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF924QYS, ENCFF930CDD, ENCFF947XIL 27293 ENCODE Processing Pipeline b8106da77faf4812f9415741a7eae9df https://www.encodeproject.org/files/ENCFF061UXU/@@download/ENCFF061UXU.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF002CVR bed narrowPeak optimal idr thresholded peaks ENCSR000DOJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens BRF1-human DNA see document see document False 2011-10-29 ENCODE 5144 ENCODE Consortium Analysis Working Group 64986bc4157feecb565adbfe599fcc07 https://www.encodeproject.org/files/ENCFF002CVR/@@download/ENCFF002CVR.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF922GRD bed narrowPeak optimal idr thresholded peaks ENCSR000EDS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MAX-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF447AAX, ENCFF617LWA, ENCFF969FOU 271367 ENCODE Processing Pipeline 4f3c95d6b517e83237e0771cb7daffc3 https://www.encodeproject.org/files/ENCFF922GRD/@@download/ENCFF922GRD.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF395KPJ bed narrowPeak optimal idr thresholded peaks ENCSR000BHP ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOSL2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF449NJO, ENCFF620ZIR, ENCFF661ITW 531483 ENCODE Processing Pipeline a2910e76c630f09cb73f1015633b84ff https://www.encodeproject.org/files/ENCFF395KPJ/@@download/ENCFF395KPJ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample ENCFF476URH bed narrowPeak optimal idr thresholded peaks ENCSR912NMR ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NONO-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF540KAO, ENCFF638XZN, ENCFF812IYD 74111 ENCODE Processing Pipeline 48db844ee2c1805a2828a25d5793f6f0 https://www.encodeproject.org/files/ENCFF476URH/@@download/ENCFF476URH.bed.gz hg19 released borderline replicate concordance ENCFF461FGJ bed narrowPeak optimal idr thresholded peaks ENCSR000BJD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RXRA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF222RUB, ENCFF455MUC, ENCFF595JYV 37777 ENCODE Processing Pipeline 47844d64dbbeff89ad267f2a4b329b58 https://www.encodeproject.org/files/ENCFF461FGJ/@@download/ENCFF461FGJ.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample insufficient read depth, poor library complexity, severe bottlenecking ENCFF713ISJ bed narrowPeak optimal idr thresholded peaks ENCSR000BPM ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour YY1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF515CEL, ENCFF697EFZ, ENCFF845YAV 301323 ENCODE Processing Pipeline e4881f3221759f989a49836abc46b388 https://www.encodeproject.org/files/ENCFF713ISJ/@@download/ENCFF713ISJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample missing control alignments ENCFF102VYH bed narrowPeak optimal idr thresholded peaks ENCSR000EWY ChIP-seq EFO:0005236 NT2/D1 cell line Homo sapiens ZNF274-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF237BUA, ENCFF562GZU, ENCFF715NVD 24193 ENCODE Processing Pipeline 83dfc249b0090c28a37144f1a52b85b5 https://www.encodeproject.org/files/ENCFF102VYH/@@download/ENCFF102VYH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF502JKO bed narrowPeak optimal idr thresholded peaks ENCSR000DYC ChIP-seq EFO:0001086 A549 cell line Homo sapiens MYC-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF511NBR, ENCFF657NEN, ENCFF878NMO 176030 ENCODE Processing Pipeline 36b284c7db5e41dcb7214b5fbfe05542 https://www.encodeproject.org/files/ENCFF502JKO/@@download/ENCFF502JKO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, inconsistent target of control experiment biological replicates with identical biosample ENCFF762DRA bed narrowPeak optimal idr thresholded peaks ENCSR000EXR ChIP-seq CL:0000765 erythroblast primary cell Homo sapiens GATA1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF039AWP, ENCFF218LZW, ENCFF535FRY 45054 ENCODE Processing Pipeline c9f963785903b49b7b904c1bc8eee567 https://www.encodeproject.org/files/ENCFF762DRA/@@download/ENCFF762DRA.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF700ILD bed narrowPeak optimal idr thresholded peaks ENCSR000DTL ChIP-seq CL:0000706 choroid plexus epithelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF009MRG, ENCFF507VHP, ENCFF680YPK 1007156 ENCODE Processing Pipeline 7b2e0a041b8477ea6dab8a9cee310a18 https://www.encodeproject.org/files/ENCFF700ILD/@@download/ENCFF700ILD.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth ENCFF002DAT bed narrowPeak optimal idr thresholded peaks ENCSR000DLN ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MYC-human DNA see document see document False 2011-03-17 ENCODE 65300 ENCODE Consortium Analysis Working Group f4de50376077a81956bb99bdc2acd914 https://www.encodeproject.org/files/ENCFF002DAT/@@download/ENCFF002DAT.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length extremely low read depth ENCFF774QKS bed narrowPeak optimal idr thresholded peaks ENCSR219BXP ChIP-seq EFO:0002067 K562 cell line Homo sapiens DPF2-human DNA False 2017-11-14 ENCODE 1, 3 ENCFF001TDO, ENCFF209OUR, ENCFF400FLC, ENCFF403MEX 479386 ENCODE Processing Pipeline cc53d3d9760a5e427276184bfc555bbe https://www.encodeproject.org/files/ENCFF774QKS/@@download/ENCFF774QKS.bed.gz hg19 released borderline replicate concordance experiment not submitted to GEO ENCFF784YVX bed narrowPeak optimal idr thresholded peaks ENCSR680OFU ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens EP300-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF023IGO, ENCFF125VLX, ENCFF467DQG 390862 ENCODE Processing Pipeline b98b1c410b37001d2fca2870513dfffb https://www.encodeproject.org/files/ENCFF784YVX/@@download/ENCFF784YVX.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, antibody characterized with exemption experiment not submitted to GEO ENCFF557KGA bed narrowPeak optimal idr thresholded peaks ENCSR000BNA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZBTB33-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF734JFJ, ENCFF770YEM, ENCFF839PVK 40188 ENCODE Processing Pipeline aeba6b6c81f68e85e8ad06ed88b5c5cc https://www.encodeproject.org/files/ENCFF557KGA/@@download/ENCFF557KGA.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF445ANP bed narrowPeak optimal idr thresholded peaks ENCSR200CUA ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens HDGF-human DNA False 2016-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF026WLK, ENCFF766QJJ, ENCFF846AFR 78411 ENCODE Processing Pipeline 667ac466c60ad43c4538ca0023c227e1 https://www.encodeproject.org/files/ENCFF445ANP/@@download/ENCFF445ANP.bed.gz hg19 released borderline replicate concordance ENCFF010UHD bed narrowPeak optimal idr thresholded peaks ENCSR968GIB ChIP-seq EFO:0002067 K562 cell line Homo sapiens RFX1-human DNA False 2016-09-20 ENCODE 3, 4 ENCFF001TDO, ENCFF163OZR, ENCFF733TAS, ENCFF786DOF 347670 ENCODE Processing Pipeline 807a6c046733e6afc5f75fcff16832d9 https://www.encodeproject.org/files/ENCFF010UHD/@@download/ENCFF010UHD.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF453CYS bed narrowPeak optimal idr thresholded peaks ENCSR261EDU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MNT-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF233WRK, ENCFF471EDO, ENCFF777ZCS 662021 ENCODE Processing Pipeline 65e3de7b1b6c017563759ecdd75a19e1 https://www.encodeproject.org/files/ENCFF453CYS/@@download/ENCFF453CYS.bed.gz hg19 released ENCFF107UHX bed narrowPeak optimal idr thresholded peaks ENCSR330OEO ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens HDAC2-human DNA False 2017-08-12 ENCODE 1, 2 ENCFF001TDO, ENCFF080QIA, ENCFF436WQE, ENCFF501TBE 29592 ENCODE Processing Pipeline 9a585121f338bdd33ad5fbf971a5b1a3 https://www.encodeproject.org/files/ENCFF107UHX/@@download/ENCFF107UHX.bed.gz hg19 released ENCFF626MVT bed narrowPeak optimal idr thresholded peaks ENCSR000EGB ChIP-seq EFO:0002067 K562 cell line Homo sapiens TBL1XR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF205BAR, ENCFF676HRI, ENCFF850MTK 276959 ENCODE Processing Pipeline 2431f6463d18398443482deaf2effc00 https://www.encodeproject.org/files/ENCFF626MVT/@@download/ENCFF626MVT.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment biological replicates with identical biosample ENCFF317TBZ bed narrowPeak optimal idr thresholded peaks ENCSR000BIR ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens SP1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF384GPX, ENCFF668CZT, ENCFF721YVP 358846 ENCODE Processing Pipeline 153f620eadc2ac2a8cf56b12fe87a91e https://www.encodeproject.org/files/ENCFF317TBZ/@@download/ENCFF317TBZ.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF690BYG bed narrowPeak optimal idr thresholded peaks ENCSR254YRM ChIP-seq UBERON:0002107 liver tissue Homo sapiens CTCF-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF181QAF, ENCFF322UFN, ENCFF543EHV 653750 ENCODE Processing Pipeline b2a17b20c503b24c30195b69ff0f22f4 https://www.encodeproject.org/files/ENCFF690BYG/@@download/ENCFF690BYG.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment experiment not submitted to GEO missing input control missing control alignments ENCFF528VFN bed narrowPeak optimal idr thresholded peaks ENCSR000DTR ChIP-seq CL:0002252 epithelial cell of esophagus primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF015JHG, ENCFF114UPJ, ENCFF301DNK 789908 ENCODE Processing Pipeline a0f666e95ff0fbc506d613ddf1c48a4a https://www.encodeproject.org/files/ENCFF528VFN/@@download/ENCFF528VFN.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms insufficient read depth missing control alignments ENCFF955YVT bed narrowPeak optimal idr thresholded peaks ENCSR899BKM ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF687-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF212CTS, ENCFF239TWK, ENCFF301EVY 372682 ENCODE Processing Pipeline f2b2b0248778f4e9e3bc207e5f52722e https://www.encodeproject.org/files/ENCFF955YVT/@@download/ENCFF955YVT.bed.gz hg19 released ENCFF027VZK bed narrowPeak optimal idr thresholded peaks ENCSR778UBR ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ARID3A-human DNA False 2017-01-31 ENCODE 5, 6 ENCFF001TDO, ENCFF644NTF, ENCFF716JVW, ENCFF877OQG 407625 ENCODE Processing Pipeline 145ef2f15c8164240d4f149dfa7e5c62 https://www.encodeproject.org/files/ENCFF027VZK/@@download/ENCFF027VZK.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF456GRS bed narrowPeak optimal idr thresholded peaks ENCSR000EFM ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens CEBPB-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF460AIN, ENCFF563ZYA, ENCFF604LSK 1353644 ENCODE Processing Pipeline 932e0d57da9a823c1dcdabd472985703 https://www.encodeproject.org/files/ENCFF456GRS/@@download/ENCFF456GRS.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF238MYM bed narrowPeak optimal idr thresholded peaks ENCSR385AHH ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF24-human DNA False 2016-04-21 ENCODE 2, 3 ENCFF001TDO, ENCFF186JNG, ENCFF420MBN, ENCFF980UAQ 280876 ENCODE Processing Pipeline e3c5e27d52c123cb162294504181685d https://www.encodeproject.org/files/ENCFF238MYM/@@download/ENCFF238MYM.bed.gz hg19 released ENCFF484CKD bed narrowPeak optimal idr thresholded peaks ENCSR000EGC ChIP-seq EFO:0002067 K562 cell line Homo sapiens RCOR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF477PXF, ENCFF620JKI, ENCFF959MXK 122282 ENCODE Processing Pipeline d8f4094f757d447fef0084be8473dbd0 https://www.encodeproject.org/files/ENCFF484CKD/@@download/ENCFF484CKD.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF447QXT bed narrowPeak optimal idr thresholded peaks ENCSR000ECF ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens RFX5-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF107RYF, ENCFF323MMZ, ENCFF577WFW 42015 ENCODE Processing Pipeline 2c4ecf570a93875da4f921f636a2e02f https://www.encodeproject.org/files/ENCFF447QXT/@@download/ENCFF447QXT.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF759MVB bed narrowPeak optimal idr thresholded peaks ENCSR513UQG ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens USF2-human DNA False 2017-06-15 ENCODE 1, 2 ENCFF001TDO, ENCFF343SNV, ENCFF362TZV, ENCFF882BWU 302978 ENCODE Processing Pipeline 5ef7807270fa0069761abc85d7009e7d https://www.encodeproject.org/files/ENCFF759MVB/@@download/ENCFF759MVB.bed.gz hg19 released file validation error, low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption mismatched file status ENCFF002COV bed narrowPeak optimal idr thresholded peaks ENCSR000EYV ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens JUND-human DNA see document see document False 2011-10-29 ENCODE 54938 ENCODE Consortium Analysis Working Group 1624be090891349e91ac01a901993f79 https://www.encodeproject.org/files/ENCFF002COV/@@download/ENCFF002COV.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF467NRS bed narrowPeak optimal idr thresholded peaks ENCSR000DNM ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFYB-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF350IOX, ENCFF655JXN, ENCFF911SLA 228205 ENCODE Processing Pipeline b44b4a58544f06561d144f4cb4004cef https://www.encodeproject.org/files/ENCFF467NRS/@@download/ENCFF467NRS.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF585YYZ bed narrowPeak optimal idr thresholded peaks ENCSR000BJC ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens dexamethasone 100 nM 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF417EBM, ENCFF576VMW, ENCFF784YSB 206771 ENCODE Processing Pipeline f00ca8d99f488bc57ab4e492958d8b45 https://www.encodeproject.org/files/ENCFF585YYZ/@@download/ENCFF585YYZ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF002CTG bed narrowPeak optimal idr thresholded peaks ENCSR000EZK ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens interferon gamma 30.0 minute STAT1-human DNA see document see document False 2011-10-29 ENCODE 345134 ENCODE Consortium Analysis Working Group dc02ec56d2dfe26638e95c008cf01f74 https://www.encodeproject.org/files/ENCFF002CTG/@@download/ENCFF002CTG.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF153JLK bed narrowPeak optimal idr thresholded peaks ENCSR000BJL ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF413BWR, ENCFF816UIF, ENCFF884SBE 82634 ENCODE Processing Pipeline cc4c628548dadf6eff641ba4393fd6fd https://www.encodeproject.org/files/ENCFF153JLK/@@download/ENCFF153JLK.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF628SBD bed narrowPeak optimal idr thresholded peaks ENCSR663ZZZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MNT-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF012KYI, ENCFF484KOR, ENCFF586OYO 622826 ENCODE Processing Pipeline da9f6a09b033a047b60fe4152bb04d96 https://www.encodeproject.org/files/ENCFF628SBD/@@download/ENCFF628SBD.bed.gz hg19 released mild to moderate bottlenecking ENCFF664ZGR bed narrowPeak optimal idr thresholded peaks ENCSR742IDN ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR2C1-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF406JPU, ENCFF497RBU, ENCFF735EGA 286705 ENCODE Processing Pipeline 99866240a9404333b974b22bd1667736 https://www.encodeproject.org/files/ENCFF664ZGR/@@download/ENCFF664ZGR.bed.gz hg19 released file validation error, mild to moderate bottlenecking, antibody characterized with exemption mismatched file status ENCFF078ATU bed narrowPeak optimal idr thresholded peaks ENCSR000BQR ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens bisphenol A 100 nM 1 hour ESR1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF887WVD, ENCFF904GCW, ENCFF986YIT 88917 ENCODE Processing Pipeline c2d7cbb3ffcb246c8d1e914492ba66b3 https://www.encodeproject.org/files/ENCFF078ATU/@@download/ENCFF078ATU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF539NTA bed narrowPeak optimal idr thresholded peaks ENCSR791AGT ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF24-human DNA False 2018-01-29 ENCODE 2, 3 ENCFF001TDO, ENCFF106XCP, ENCFF415JVE, ENCFF852WZC 129205 ENCODE Processing Pipeline bf9b021386c9ca484566857247f651cb https://www.encodeproject.org/files/ENCFF539NTA/@@download/ENCFF539NTA.bed.gz hg19 released experiment not submitted to GEO ENCFF810CEL bed narrowPeak optimal idr thresholded peaks ENCSR514VYD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NR2F1-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF241KMD, ENCFF766CJW, ENCFF878DLA 755749 ENCODE Processing Pipeline 6f809f7b7c61d376d524f1789d35c3dd https://www.encodeproject.org/files/ENCFF810CEL/@@download/ENCFF810CEL.bed.gz hg19 released mild to moderate bottlenecking ENCFF808WQI bed narrowPeak optimal idr thresholded peaks ENCSR029IBC ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ARNT-human DNA False 2017-01-31 ENCODE 1, 2 ENCFF001TDO, ENCFF078MLZ, ENCFF409LKX, ENCFF469FRK 24535 ENCODE Processing Pipeline 0abe74aad8be20ae1d2cdd97ab5fb152 https://www.encodeproject.org/files/ENCFF808WQI/@@download/ENCFF808WQI.bed.gz hg19 released borderline replicate concordance ENCFF706RIA bed narrowPeak optimal idr thresholded peaks ENCSR000EDQ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RCOR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF119GVR, ENCFF531FFM, ENCFF827IXZ 101271 ENCODE Processing Pipeline 6d0a14b130b1f915375be8647eed081c https://www.encodeproject.org/files/ENCFF706RIA/@@download/ENCFF706RIA.bed.gz hg19 released low read length, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF015YHT bed narrowPeak optimal idr thresholded peaks ENCSR342THD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BCLAF1-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF082QVO, ENCFF222GJV, ENCFF308RFY 53338 ENCODE Processing Pipeline a8cfce2cd4f95a90ebe3f1b1704ea0a7 https://www.encodeproject.org/files/ENCFF015YHT/@@download/ENCFF015YHT.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity, antibody characterized with exemption ENCFF273TYA bed narrowPeak optimal idr thresholded peaks ENCSR249BHQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF592-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF322TVZ, ENCFF363AAC, ENCFF537WLH 662184 ENCODE Processing Pipeline c8ba92b030fc5472424b29f32f637dc7 https://www.encodeproject.org/files/ENCFF273TYA/@@download/ENCFF273TYA.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF258RWN bed narrowPeak optimal idr thresholded peaks ENCSR359LOD ChIP-seq EFO:0002074 PC-3 cell line Homo sapiens CTCF-human DNA see document see document False 2017-10-19 ENCODE 1, 2 ENCFF001TDO, ENCFF646CMN, ENCFF752ZNY, ENCFF888CCA 1222113 ENCODE Processing Pipeline 56a529d11450f4ff7814d1699245ec5f https://www.encodeproject.org/files/ENCFF258RWN/@@download/ENCFF258RWN.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF530FZL bed narrowPeak optimal idr thresholded peaks ENCSR189VXS ChIP-seq EFO:0002067 K562 cell line Homo sapiens GTF2F1-human DNA False 2018-01-30 ENCODE 1, 2 ENCFF001TDO, ENCFF007QMQ, ENCFF601KTD, ENCFF846SYJ 329728 ENCODE Processing Pipeline 777dde87a6c7533afb8183cab4ad171f https://www.encodeproject.org/files/ENCFF530FZL/@@download/ENCFF530FZL.bed.gz hg19 released experiment not submitted to GEO partially characterized antibody ENCFF240PYU bed narrowPeak optimal idr thresholded peaks ENCSR906PEI ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens SP1-human DNA False 2017-05-18 ENCODE 1, 2 ENCFF001TDO, ENCFF333AFS, ENCFF713XLB, ENCFF730EIH 22954 ENCODE Processing Pipeline 94f3b9561dab2bf41b16692b087cccd7 https://www.encodeproject.org/files/ENCFF240PYU/@@download/ENCFF240PYU.bed.gz hg19 released ENCFF653ZMJ bed narrowPeak optimal idr thresholded peaks ENCSR756ZKG ChIP-seq EFO:0006710 OCI-LY3 cell line Homo sapiens CTCF-human DNA see document see document False 2014-07-11 ENCODE 1, 2 ENCFF001TDO, ENCFF662BPG, ENCFF763SUY, ENCFF935FTJ 935049 ENCODE Processing Pipeline 39fc52436e5ef8b2ecdc550dde48f11d https://www.encodeproject.org/files/ENCFF653ZMJ/@@download/ENCFF653ZMJ.bed.gz hg19 released low read length, low read depth, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF195ODE bed narrowPeak optimal idr thresholded peaks ENCSR557RVF ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZHX1-human DNA False 2014-07-07 ENCODE 1, 3 ENCFF001TDO, ENCFF194DPB, ENCFF608GUA, ENCFF924ENQ 66009 ENCODE Processing Pipeline a1e2f7cfe616efa0fd80d7f1210ba11f https://www.encodeproject.org/files/ENCFF195ODE/@@download/ENCFF195ODE.bed.gz hg19 released low read length, low read depth ENCFF769NCM bed narrowPeak optimal idr thresholded peaks ENCSR046HGP ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens EZH2-human DNA False 2017-11-18 ENCODE 1, 2 ENCFF001TDO, ENCFF014MFB, ENCFF782VWT, ENCFF905USH 13732 ENCODE Processing Pipeline 81fa11809db03d52ce78b886f3c317fc https://www.encodeproject.org/files/ENCFF769NCM/@@download/ENCFF769NCM.bed.gz hg19 released mixed run types, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF372DRC bed narrowPeak optimal idr thresholded peaks ENCSR000DZU ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens USF2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF023RDZ, ENCFF485PHV, ENCFF548FHH 139589 ENCODE Processing Pipeline c0e28ff4091658d0e94ba0a69b97e145 https://www.encodeproject.org/files/ENCFF372DRC/@@download/ENCFF372DRC.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF127GYQ bed narrowPeak optimal idr thresholded peaks ENCSR961PPA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ATF2-human DNA False 2016-10-26 ENCODE 1, 2 ENCFF001TDO, ENCFF147CFU, ENCFF301WWU, ENCFF869LKG 340897 ENCODE Processing Pipeline 0ac1a8c909c53b83c0eab8dd64d2ff69 https://www.encodeproject.org/files/ENCFF127GYQ/@@download/ENCFF127GYQ.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF161PGD bed narrowPeak optimal idr thresholded peaks ENCSR112ALD ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CREB1-human DNA False 2017-11-14 ENCODE 2, 3 ENCFF001TDO, ENCFF365ROK, ENCFF708DXF, ENCFF732KKY 753611 ENCODE Processing Pipeline 8cffc6ccd34129dc10ef7665da0c304d https://www.encodeproject.org/files/ENCFF161PGD/@@download/ENCFF161PGD.bed.gz hg19 released experiment not submitted to GEO ENCFF968JVX bed narrowPeak optimal idr thresholded peaks ENCSR395HWC ChIP-seq EFO:0002067 K562 cell line Homo sapiens IKZF1-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF038VEX, ENCFF669ACI, ENCFF723ESB 853540 ENCODE Processing Pipeline 684bdc0057a6241a64f889a8afb4cd56 https://www.encodeproject.org/files/ENCFF968JVX/@@download/ENCFF968JVX.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF997AAW bed narrowPeak optimal idr thresholded peaks ENCSR529JYA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens HCFC1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF103LIH, ENCFF708LWT, ENCFF738IWJ 112216 ENCODE Processing Pipeline 53a70ccc5c4326fe942b548aae05eb6b https://www.encodeproject.org/files/ENCFF997AAW/@@download/ENCFF997AAW.bed.gz hg19 released low read length, low read depth ENCFF988HJD bed narrowPeak optimal idr thresholded peaks ENCSR000DON ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens afimoxifene 1.0 μM 36.0 hour FOS-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF215QRX, ENCFF494HZF, ENCFF639ZSQ 1252109 ENCODE Processing Pipeline bddbf848bde7839ac92b90dde93d3edf https://www.encodeproject.org/files/ENCFF988HJD/@@download/ENCFF988HJD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample, duplicate lane review missing control alignments ENCFF544CYG bed narrowPeak optimal idr thresholded peaks ENCSR801SWX ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens TARDBP-human DNA False 2017-02-01 ENCODE 1, 2 ENCFF001TDO, ENCFF319FAG, ENCFF411PFB, ENCFF480TTE 222654 ENCODE Processing Pipeline 00341568066ea40847437d46812194c5 https://www.encodeproject.org/files/ENCFF544CYG/@@download/ENCFF544CYG.bed.gz hg19 released ENCFF974OIC bed narrowPeak optimal idr thresholded peaks ENCSR407BEZ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZHX2-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF236YIV, ENCFF392FYA, ENCFF640NJO 181311 ENCODE Processing Pipeline 79e70a2005e90b9615aa7013c7effab6 https://www.encodeproject.org/files/ENCFF974OIC/@@download/ENCFF974OIC.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF733UTZ bed narrowPeak optimal idr thresholded peaks ENCSR412QBS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TARDBP-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF016QUV, ENCFF187SWR, ENCFF354CAT 438542 ENCODE Processing Pipeline 857832d61646de57b072948b6b33b410 https://www.encodeproject.org/files/ENCFF733UTZ/@@download/ENCFF733UTZ.bed.gz hg19 released ENCFF965BBC bed narrowPeak optimal idr thresholded peaks ENCSR000DQD ChIP-seq EFO:0005725 BE2C cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF082FUL, ENCFF535IOO, ENCFF863FFV 905006 ENCODE Processing Pipeline b391745a29366760d1126d5c58fd8512 https://www.encodeproject.org/files/ENCFF965BBC/@@download/ENCFF965BBC.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF136BEY bed narrowPeak optimal idr thresholded peaks ENCSR000DMS ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens 17β-estradiol 100 nM 45 minute CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF007EZA, ENCFF217YFS, ENCFF438DXI 1074391 ENCODE Processing Pipeline f0937e8a61eef201006009516fe71acb https://www.encodeproject.org/files/ENCFF136BEY/@@download/ENCFF136BEY.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample missing control alignments ENCFF527ALV bed narrowPeak optimal idr thresholded peaks ENCSR391KQC ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MTA3-human DNA False 2016-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF257ALC, ENCFF402AKR, ENCFF434NPI 78206 ENCODE Processing Pipeline cb10f87e27dba429bc70867de4e6c85a https://www.encodeproject.org/files/ENCFF527ALV/@@download/ENCFF527ALV.bed.gz hg19 released borderline replicate concordance ENCFF116RLU bed narrowPeak optimal idr thresholded peaks ENCSR000HPG ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens SMC3-human DNA False 2016-10-26 ENCODE 1, 3 ENCFF001TDO, ENCFF551KOG, ENCFF603HVK, ENCFF925XIR 561934 ENCODE Processing Pipeline df3a18ae7973dc03e024e724ccaf3c13 https://www.encodeproject.org/files/ENCFF116RLU/@@download/ENCFF116RLU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption ENCFF308ZGG bed narrowPeak optimal idr thresholded peaks ENCSR009MBP ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens HSF1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF421XER, ENCFF607QZV, ENCFF618CLL 47623 ENCODE Processing Pipeline 855faa28674750c111acec0d56d5d750 https://www.encodeproject.org/files/ENCFF308ZGG/@@download/ENCFF308ZGG.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF002CSK bed narrowPeak optimal idr thresholded peaks ENCSR000EVI ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ELK4-human DNA see document see document False 2011-10-29 ENCODE 135202 ENCODE Consortium Analysis Working Group 5b840f06ad48a31dffba2764ce3f40ec https://www.encodeproject.org/files/ENCFF002CSK/@@download/ENCFF002CSK.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF397XTF bed narrowPeak optimal idr thresholded peaks ENCSR318LVG ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZBTB40-human DNA False 2016-09-20 ENCODE 1, 2 ENCFF001TDO, ENCFF086HCP, ENCFF511ZHC, ENCFF685HYH 275891 ENCODE Processing Pipeline a71767d139b97728bef6593298a3d875 https://www.encodeproject.org/files/ENCFF397XTF/@@download/ENCFF397XTF.bed.gz hg19 released file validation error, mild to moderate bottlenecking mismatched file status ENCFF208TRU bed narrowPeak optimal idr thresholded peaks ENCSR514VAY ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens HCFC1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF251KCB, ENCFF567MQM, ENCFF894EBL 167235 ENCODE Processing Pipeline b6b7a380d838641fb514a9c1fd6b89e3 https://www.encodeproject.org/files/ENCFF208TRU/@@download/ENCFF208TRU.bed.gz hg19 released low read length ENCFF054LVE bed narrowPeak optimal idr thresholded peaks ENCSR946ZLI ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-KLF13-human DNA formaldehyde False 2017-11-30 ENCODE 1, 2 ENCFF001TDO, ENCFF468YQB, ENCFF495ICA, ENCFF742QVY 181804 ENCODE Processing Pipeline 5bc33b794fbae98252426d8ca90bfad6 https://www.encodeproject.org/files/ENCFF054LVE/@@download/ENCFF054LVE.bed.gz hg19 released low read depth, missing genetic modification characterization experiment not submitted to GEO missing control alignments ENCFF683KBO bed narrowPeak optimal idr thresholded peaks ENCSR066EBK ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXA2-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF144UTI, ENCFF516CRP, ENCFF532LNM 1245223 ENCODE Processing Pipeline cc14e80a87319acc940932944771f108 https://www.encodeproject.org/files/ENCFF683KBO/@@download/ENCFF683KBO.bed.gz hg19 released ENCFF502ZTC bed narrowPeak optimal idr thresholded peaks ENCSR047BUZ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ATF2-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF474JRH, ENCFF731IFM, ENCFF750HPK 1135631 ENCODE Processing Pipeline a6a22b8d5cf6d58a3a27d3b0952f7874 https://www.encodeproject.org/files/ENCFF502ZTC/@@download/ENCFF502ZTC.bed.gz hg19 released borderline replicate concordance ENCFF081JNO bed narrowPeak optimal idr thresholded peaks ENCSR000BKJ ChIP-seq EFO:0002785 GM12891 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF505NSP, ENCFF519AMH, ENCFF994XKT 295188 ENCODE Processing Pipeline abed55987806d18a1d2d5f121536c7ac https://www.encodeproject.org/files/ENCFF081JNO/@@download/ENCFF081JNO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF126PJF bed narrowPeak optimal idr thresholded peaks ENCSR155VDK ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZBTB11-human DNA False 2016-04-25 ENCODE 1, 2 ENCFF001TDO, ENCFF224PZN, ENCFF321JQC, ENCFF627DPA 42359 ENCODE Processing Pipeline 1cbb892e070ba237950c699124a9f18a https://www.encodeproject.org/files/ENCFF126PJF/@@download/ENCFF126PJF.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption ENCFF708OJJ bed narrowPeak optimal idr thresholded peaks ENCSR887MXT ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZHX1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF436EXX, ENCFF695CJR, ENCFF698USR 60464 ENCODE Processing Pipeline 1da1a1c1a4cddbaa11dbd4fb1ae9a963 https://www.encodeproject.org/files/ENCFF708OJJ/@@download/ENCFF708OJJ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth ENCFF725LDD bed narrowPeak optimal idr thresholded peaks ENCSR000BIV ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens SRF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF145RHD, ENCFF471LWP, ENCFF605EQP 99200 ENCODE Processing Pipeline 9650ba5ad4127ecca39d1e2d2efc50e9 https://www.encodeproject.org/files/ENCFF725LDD/@@download/ENCFF725LDD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF086LMU bed narrowPeak optimal idr thresholded peaks ENCSR771GTF ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens SUZ12-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF186LIR, ENCFF381HBX, ENCFF558TFD 37524 ENCODE Processing Pipeline 749996d8fe43925ce133918d367e2c7b https://www.encodeproject.org/files/ENCFF086LMU/@@download/ENCFF086LMU.bed.gz hg19 released low read length, low read depth ENCFF712LMP bed narrowPeak optimal idr thresholded peaks ENCSR707IUN ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens NFE2L2-human DNA False 2016-08-31 ENCODE 1, 2 ENCFF001TDO, ENCFF249ESZ, ENCFF445YDK, ENCFF737CTQ 138212 ENCODE Processing Pipeline 71a63bdc531b0c8197e1fc6c7d385ab9 https://www.encodeproject.org/files/ENCFF712LMP/@@download/ENCFF712LMP.bed.gz hg19 released low read length, low read depth ENCFF266KSD bed narrowPeak optimal idr thresholded peaks ENCSR752NDX ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF282-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF165DIG, ENCFF313GGY, ENCFF719GJP 40174 ENCODE Processing Pipeline 166fa526550204b365512e1d5ada00c2 https://www.encodeproject.org/files/ENCFF266KSD/@@download/ENCFF266KSD.bed.gz hg19 released borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF710VEH bed narrowPeak optimal idr thresholded peaks ENCSR000DZN ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CTCF-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF256QBB, ENCFF307KRD, ENCFF833GQU 702399 ENCODE Processing Pipeline cc13297e7415d8e276f3516031835828 https://www.encodeproject.org/files/ENCFF710VEH/@@download/ENCFF710VEH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample control insufficient read depth, insufficient read depth ENCFF549GMO bed narrowPeak optimal idr thresholded peaks ENCSR223MLH ChIP-seq EFO:0002067 K562 cell line Homo sapiens BRCA1-human DNA False 2017-05-18 ENCODE 1, 2 ENCFF001TDO, ENCFF248TTW, ENCFF302RJE, ENCFF507JPU 18922 ENCODE Processing Pipeline df978590cd462b0053dd3bfc64f17142 https://www.encodeproject.org/files/ENCFF549GMO/@@download/ENCFF549GMO.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF261XPP bed narrowPeak optimal idr thresholded peaks ENCSR033VAZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens TARDBP-human DNA False 2016-04-22 ENCODE 2, 3 ENCFF001TDO, ENCFF506ZBZ, ENCFF612BYB, ENCFF654INX 242184 ENCODE Processing Pipeline ac65d03826f780526495ec873aa0d673 https://www.encodeproject.org/files/ENCFF261XPP/@@download/ENCFF261XPP.bed.gz hg19 released ENCFF603MCO bed narrowPeak optimal idr thresholded peaks ENCSR000BTF ChIP-seq EFO:0002793 HL-60 cell line Homo sapiens REST-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF152FPH, ENCFF427PNP, ENCFF955CMQ 250253 ENCODE Processing Pipeline bd65a9b594a044fa6e72d0baca077e59 https://www.encodeproject.org/files/ENCFF603MCO/@@download/ENCFF603MCO.bed.gz hg19 released low read depth biological replicates with identical biosample insufficient replicate concordance ENCFF970AVM bed narrowPeak optimal idr thresholded peaks ENCSR000DPG ChIP-seq NTR:0000478 AG04449 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF252SGK, ENCFF671VPQ, ENCFF738FKM 774670 ENCODE Processing Pipeline f04834aa1a9828e037a2d125449602be https://www.encodeproject.org/files/ENCFF970AVM/@@download/ENCFF970AVM.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity NTR biosample insufficient read depth missing control alignments ENCFF925MHB bed narrowPeak optimal idr thresholded peaks ENCSR618GDK ChIP-seq EFO:0002067 K562 cell line Homo sapiens CEBPZ-human DNA False 2014-07-07 ENCODE 1, 4 ENCFF001TDO, ENCFF355FJN, ENCFF830WTR, ENCFF895ZCE 24634 ENCODE Processing Pipeline 883e9c0b1e68c25bad97a58920ac3f58 https://www.encodeproject.org/files/ENCFF925MHB/@@download/ENCFF925MHB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance ENCFF765BRD bed narrowPeak optimal idr thresholded peaks ENCSR987GXT ChIP-seq EFO:0007950 GM23338 induced pluripotent stem cell line Homo sapiens CTCF-human DNA False 2017-10-19 ENCODE 1, 2 ENCFF001TDO, ENCFF214JLG, ENCFF236MQY, ENCFF651CJJ 1262132 ENCODE Processing Pipeline 5910eb61c8a1c3124666845d4245da27 https://www.encodeproject.org/files/ENCFF765BRD/@@download/ENCFF765BRD.bed.gz hg19 released mild to moderate bottlenecking, low read depth, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF545SXB bed narrowPeak optimal idr thresholded peaks ENCSR778QLY ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens ELF4-human DNA False 2017-01-31 ENCODE 1, 2 ENCFF001TDO, ENCFF280LRQ, ENCFF480NXP, ENCFF802MVF 118104 ENCODE Processing Pipeline 2a018e52c7336d6fcce93715a481d388 https://www.encodeproject.org/files/ENCFF545SXB/@@download/ENCFF545SXB.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF002CSI bed narrowPeak optimal idr thresholded peaks ENCSR000EVK ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens E2F6-human DNA see document see document False 2011-10-29 ENCODE 117604 ENCODE Consortium Analysis Working Group 768813aca230dfe904b00a36c6cffdcd https://www.encodeproject.org/files/ENCFF002CSI/@@download/ENCFF002CSI.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF030BPR bed narrowPeak optimal idr thresholded peaks ENCSR857PBV ChIP-seq EFO:0002095 22Rv1 cell line Homo sapiens CTCF-human DNA False 2017-06-15 ENCODE 1, 2 ENCFF001TDO, ENCFF144QCV, ENCFF615UXP, ENCFF887CGM 1588398 ENCODE Processing Pipeline 5f43fb71d39e6aca7ccb6aef19451ff0 https://www.encodeproject.org/files/ENCFF030BPR/@@download/ENCFF030BPR.bed.gz hg19 released mild to moderate bottlenecking NTR biosample ENCFF510UBQ bed narrowPeak optimal idr thresholded peaks ENCSR867WPH ChIP-seq UBERON:0002107 liver tissue Homo sapiens REST-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF034ALK, ENCFF501HAG, ENCFF783JKF 638782 ENCODE Processing Pipeline 047d4008e34b135f96b20243b80c4441 https://www.encodeproject.org/files/ENCFF510UBQ/@@download/ENCFF510UBQ.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF417LEJ bed narrowPeak optimal idr thresholded peaks ENCSR237VLT ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZBTB40-human DNA False 2016-08-01 ENCODE 1, 2 ENCFF001TDO, ENCFF361LXO, ENCFF707CDO, ENCFF727WJU 563762 ENCODE Processing Pipeline ee5c6e2a9253142ea4ec418a2668994d https://www.encodeproject.org/files/ENCFF417LEJ/@@download/ENCFF417LEJ.bed.gz hg19 released ENCFF932EVL bed narrowPeak optimal idr thresholded peaks ENCSR831EIW ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens FOXM1-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF141MCC, ENCFF618BDU, ENCFF644PFR 102472 ENCODE Processing Pipeline 8324015652ce03e8a0be6cd9278a3f2a https://www.encodeproject.org/files/ENCFF932EVL/@@download/ENCFF932EVL.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF741WKY bed narrowPeak optimal idr thresholded peaks ENCSR000BJX ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens SP1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF121SXP, ENCFF420CVJ, ENCFF740QPT 593220 ENCODE Processing Pipeline 637ee87b99d565855508c0e4d6d3c2d8 https://www.encodeproject.org/files/ENCFF741WKY/@@download/ENCFF741WKY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient replicate concordance missing control alignments ENCFF195IKR bed narrowPeak optimal idr thresholded peaks ENCSR000BIM ChIP-seq EFO:0002785 GM12891 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF257RXE, ENCFF893QMD, ENCFF994IJB 269898 ENCODE Processing Pipeline ff7eec22f7f6ea26a65ebf19c5976fda https://www.encodeproject.org/files/ENCFF195IKR/@@download/ENCFF195IKR.bed.gz hg19 released control low read depth, low read length, low read depth biological replicates with identical biosample missing control alignments ENCFF058XAD bed narrowPeak optimal idr thresholded peaks ENCSR000BMX ChIP-seq EFO:0001247 T47D cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour GATA3-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF368ICR, ENCFF370FVF, ENCFF591LXN 775431 ENCODE Processing Pipeline 0698eb75edf612f795a48307b318d11f https://www.encodeproject.org/files/ENCFF058XAD/@@download/ENCFF058XAD.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF028BDC bed narrowPeak optimal idr thresholded peaks ENCSR000BID ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens BHLHE40-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF215GXO, ENCFF333ZRM, ENCFF626BVG 61955 ENCODE Processing Pipeline a5acbe34ad3e7ba0f7923a00120943fc https://www.encodeproject.org/files/ENCFF028BDC/@@download/ENCFF028BDC.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth, poor library complexity, severe bottlenecking missing control alignments ENCFF824FIL bed narrowPeak optimal idr thresholded peaks ENCSR000BLD ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens RAD21-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF216OCU, ENCFF428PSB, ENCFF474BFW 1187834 ENCODE Processing Pipeline 23e386dd5736b37be6fee217c9b4406b https://www.encodeproject.org/files/ENCFF824FIL/@@download/ENCFF824FIL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity biological replicates with identical biosample missing control alignments ENCFF303TVZ bed narrowPeak optimal idr thresholded peaks ENCSR000DZX ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens IRF3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF271PVK, ENCFF434CQV, ENCFF678BIU 36479 ENCODE Processing Pipeline 814f0bb635cc8a5600eb2018921ab663 https://www.encodeproject.org/files/ENCFF303TVZ/@@download/ENCFF303TVZ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF784FIE bed narrowPeak optimal idr thresholded peaks ENCSR325DER ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR3C1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF037BJD, ENCFF261TNJ, ENCFF793DLG 46890 ENCODE Processing Pipeline 27585931a99c4d1c463cb076f662bc3b https://www.encodeproject.org/files/ENCFF784FIE/@@download/ENCFF784FIE.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity experiment not submitted to GEO partially characterized antibody ENCFF184RRU bed narrowPeak optimal idr thresholded peaks ENCSR670FDA ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFATC3-human DNA False 2017-09-29 ENCODE 1, 2 ENCFF001TDO, ENCFF324WHA, ENCFF620EBO, ENCFF951XWI 133041 ENCODE Processing Pipeline 3ae96e984e743858b619938ccc58a435 https://www.encodeproject.org/files/ENCFF184RRU/@@download/ENCFF184RRU.bed.gz hg19 released mild to moderate bottlenecking ENCFF558JBX bed narrowPeak optimal idr thresholded peaks ENCSR024CNP ChIP-seq EFO:0002067 K562 cell line Homo sapiens EGR1-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF255VCC, ENCFF637AOG, ENCFF782FAJ 605717 ENCODE Processing Pipeline 8149a5a796a465fc5a678edf965522ce https://www.encodeproject.org/files/ENCFF558JBX/@@download/ENCFF558JBX.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF073PCP bed narrowPeak optimal idr thresholded peaks ENCSR000BKP ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens JUND-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF041GFP, ENCFF686SJD, ENCFF905FMJ 258230 ENCODE Processing Pipeline 009fcd86b3b4d6d1e42350f2b7f87273 https://www.encodeproject.org/files/ENCFF073PCP/@@download/ENCFF073PCP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample poor library complexity, severe bottlenecking ENCFF002CTN bed narrowPeak optimal idr thresholded peaks ENCSR000ECW ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens USF2-human DNA see document see document False 2011-10-29 ENCODE 311276 ENCODE Consortium Analysis Working Group 333a8fbc667b992f645fbede4a5501c8 https://www.encodeproject.org/files/ENCFF002CTN/@@download/ENCFF002CTN.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF350YXB bed narrowPeak optimal idr thresholded peaks ENCSR914NEI ChIP-seq EFO:0002067 K562 cell line Homo sapiens MTA3-human DNA formaldehyde False 2017-06-07 ENCODE 2, 3 ENCFF001TDO, ENCFF326WKP, ENCFF883SHN, ENCFF976RBY 528070 ENCODE Processing Pipeline 3ea3ef0e96deacc4e08f7eb62dbcdac3 https://www.encodeproject.org/files/ENCFF350YXB/@@download/ENCFF350YXB.bed.gz hg19 released mild to moderate bottlenecking ENCFF020GMZ bed narrowPeak optimal idr thresholded peaks ENCSR711XNY ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens PKNOX1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF049YTC, ENCFF583BIS, ENCFF825QFX 624856 ENCODE Processing Pipeline 12bb6684c3e7567ee87c6ac3c7b4af68 https://www.encodeproject.org/files/ENCFF020GMZ/@@download/ENCFF020GMZ.bed.gz hg19 released mild to moderate bottlenecking ENCFF596OJV bed narrowPeak optimal idr thresholded peaks ENCSR126YEB ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens FOXA1-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF017WRM, ENCFF031CJZ, ENCFF565ZVL 661291 ENCODE Processing Pipeline 54fbe703b1a67e989d62a1761ae130d5 https://www.encodeproject.org/files/ENCFF596OJV/@@download/ENCFF596OJV.bed.gz hg19 released low read depth ENCFF641RNZ bed narrowPeak optimal idr thresholded peaks ENCSR197WGI ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens NFE2L2-human DNA False 2016-09-01 ENCODE 2, 3 ENCFF001TDO, ENCFF777LPB, ENCFF917EWZ, ENCFF950ARZ 275301 ENCODE Processing Pipeline 23071fd9061c37180996a41abc7793ae https://www.encodeproject.org/files/ENCFF641RNZ/@@download/ENCFF641RNZ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF514OOQ bed narrowPeak optimal idr thresholded peaks ENCSR218GSN ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens ZFX-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF266JIG, ENCFF694AUF, ENCFF762KYA 438040 ENCODE Processing Pipeline b1370f2dae4b9b958efb4b081343162b https://www.encodeproject.org/files/ENCFF514OOQ/@@download/ENCFF514OOQ.bed.gz hg19 released antibody characterized with exemption NTR biosample ENCFF782KFG bed narrowPeak optimal idr thresholded peaks ENCSR402IDP ChIP-seq EFO:0005724 MM.1S cell line Homo sapiens CTCF-human DNA False 2016-08-11 ENCODE 1, 2 ENCFF001TDO, ENCFF507RFD, ENCFF691NVX, ENCFF974RFW 751199 ENCODE Processing Pipeline 0c81256878b5c45a50617e772db57427 https://www.encodeproject.org/files/ENCFF782KFG/@@download/ENCFF782KFG.bed.gz hg19 released low read length, antibody characterized with exemption, mixed read lengths NTR biosample ENCFF521CRG bed narrowPeak optimal idr thresholded peaks ENCSR776CYN ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZFP36-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF233END, ENCFF688ELV, ENCFF734ODE 361453 ENCODE Processing Pipeline 8905c7dc4614bdddbe70d643dae0973b https://www.encodeproject.org/files/ENCFF521CRG/@@download/ENCFF521CRG.bed.gz hg19 released low read length, low read depth experiment not submitted to GEO partially characterized antibody ENCFF706LIT bed narrowPeak optimal idr thresholded peaks ENCSR107RHZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens YBX1-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF609DTK, ENCFF669CKL, ENCFF749VLH 26921 ENCODE Processing Pipeline 1fde054e4ffdaa0d943623283ebc001a https://www.encodeproject.org/files/ENCFF706LIT/@@download/ENCFF706LIT.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF163VUK bed narrowPeak optimal idr thresholded peaks ENCSR882ERE ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZKSCAN1-human DNA False 2016-03-02 ENCODE 1, 2 ENCFF001TDO, ENCFF040DGA, ENCFF511MUZ, ENCFF656CUX 217692 ENCODE Processing Pipeline c743b22b355085c49a0ee67adfa8f5f2 https://www.encodeproject.org/files/ENCFF163VUK/@@download/ENCFF163VUK.bed.gz hg19 released low read length, low read depth ENCFF549KOD bed narrowPeak optimal idr thresholded peaks ENCSR547LKC ChIP-seq EFO:0002067 K562 cell line Homo sapiens GATAD2B-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF198CPZ, ENCFF418WIA, ENCFF849HOO 250332 ENCODE Processing Pipeline 4c6d59eb2d9fee9bb959881542988713 https://www.encodeproject.org/files/ENCFF549KOD/@@download/ENCFF549KOD.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF068DLY bed narrowPeak optimal idr thresholded peaks ENCSR702GMW ChIP-seq EFO:0002847 PC-9 cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF432ZMO, ENCFF555PRT, ENCFF614KPG 89185 ENCODE Processing Pipeline 9a66417c7c7a963da54869ff4eff870e https://www.encodeproject.org/files/ENCFF068DLY/@@download/ENCFF068DLY.bed.gz hg19 released low read depth, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF944GZI bed narrowPeak optimal idr thresholded peaks ENCSR669NFS ChIP-seq EFO:0002067 K562 cell line Homo sapiens ARNT-human DNA False 2018-01-26 ENCODE 3, 4 ENCFF001TDO, ENCFF286UPH, ENCFF333QJD, ENCFF968TKP 115274 ENCODE Processing Pipeline 047a545f5de7e170d1e06e9dfe3ee10a https://www.encodeproject.org/files/ENCFF944GZI/@@download/ENCFF944GZI.bed.gz hg19 released mild to moderate bottlenecking, low read depth experiment not submitted to GEO partially characterized antibody ENCFF392MUM bed narrowPeak optimal idr thresholded peaks ENCSR502OEK ChIP-seq EFO:0002067 K562 cell line Homo sapiens ELF1-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF725PEY, ENCFF813JVU, ENCFF883ZAE 271048 ENCODE Processing Pipeline feec5c83ee0073bfeead5b1f269e553f https://www.encodeproject.org/files/ENCFF392MUM/@@download/ENCFF392MUM.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF523NXP bed narrowPeak optimal idr thresholded peaks ENCSR237TFX ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens CTBP1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF031LVS, ENCFF094ESY, ENCFF851UVY 160167 ENCODE Processing Pipeline bc4c1b6642b6d7699879f3ae0fdc01fe https://www.encodeproject.org/files/ENCFF523NXP/@@download/ENCFF523NXP.bed.gz hg19 released borderline replicate concordance ENCFF146XEP bed narrowPeak optimal idr thresholded peaks ENCSR094WHO ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens FOXA1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF288DTP, ENCFF329TNA, ENCFF893RQA 25374 ENCODE Processing Pipeline adde07d94f68bcd1be893e272c83d9a1 https://www.encodeproject.org/files/ENCFF146XEP/@@download/ENCFF146XEP.bed.gz hg19 released mild to moderate bottlenecking ENCFF298UPI bed narrowPeak optimal idr thresholded peaks ENCSR459FTB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens UBTF-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF191TQD, ENCFF688WOB, ENCFF878ZPT 28532 ENCODE Processing Pipeline c82f947c982c796763283fc21f4ad097 https://www.encodeproject.org/files/ENCFF298UPI/@@download/ENCFF298UPI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance ENCFF315VQM bed narrowPeak optimal idr thresholded peaks ENCSR897MYK ChIP-seq EFO:0001086 A549 cell line Homo sapiens SREBF1-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF290WHA, ENCFF491WEZ, ENCFF926IPE 68730 ENCODE Processing Pipeline 52c030c2d14a1c8c5aff2675d1e82050 https://www.encodeproject.org/files/ENCFF315VQM/@@download/ENCFF315VQM.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption ENCFF567GSX bed narrowPeak optimal idr thresholded peaks ENCSR512NLO ChIP-seq EFO:0002067 K562 cell line Homo sapiens MNT-human DNA False 2017-05-17 ENCODE 1, 2 ENCFF001TDO, ENCFF595GHN, ENCFF799NMK, ENCFF846YPA 542551 ENCODE Processing Pipeline dade819d689c4ea2e878e83004ee4f3b https://www.encodeproject.org/files/ENCFF567GSX/@@download/ENCFF567GSX.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF870CER bed narrowPeak optimal idr thresholded peaks ENCSR197DJH ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens SREBF1-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF225KYS, ENCFF531PCT, ENCFF642ZUX 194548 ENCODE Processing Pipeline cf46823662aa528fb2ccec35723bccae https://www.encodeproject.org/files/ENCFF870CER/@@download/ENCFF870CER.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF920HDC bed narrowPeak optimal idr thresholded peaks ENCSR347NOB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CEBPZ-human DNA False 2016-03-02 ENCODE 1, 3 ENCFF001TDO, ENCFF045PNJ, ENCFF140CXA, ENCFF932DYK 20648 ENCODE Processing Pipeline e61bfccca114033dcdd022214dce007f https://www.encodeproject.org/files/ENCFF920HDC/@@download/ENCFF920HDC.bed.gz hg19 released low read length, low read depth ENCFF043YZF bed narrowPeak optimal idr thresholded peaks ENCSR832OGB ChIP-seq EFO:0002067 K562 cell line Homo sapiens LEF1-human DNA False 2017-05-17 ENCODE 3, 4 ENCFF001TDO, ENCFF404ZDG, ENCFF700RYG, ENCFF804WBF 98778 ENCODE Processing Pipeline 35c35430c78f681d42182db300ec48a9 https://www.encodeproject.org/files/ENCFF043YZF/@@download/ENCFF043YZF.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF640ORY bed narrowPeak optimal idr thresholded peaks ENCSR184MFH ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZFP36-human DNA False 2014-07-07 ENCODE 1, 3 ENCFF001TDO, ENCFF233ITG, ENCFF491ZMR, ENCFF979YOQ 61240 ENCODE Processing Pipeline 9e4bcfd497cd57be71e9c3fccf8aba30 https://www.encodeproject.org/files/ENCFF640ORY/@@download/ENCFF640ORY.bed.gz hg19 released low read length, low read depth experiment not submitted to GEO partially characterized antibody ENCFF266ORV bed narrowPeak optimal idr thresholded peaks ENCSR473SUA ChIP-seq EFO:0001086 A549 cell line Homo sapiens ESRRA-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF391VQJ, ENCFF705XME, ENCFF804JRA 49062 ENCODE Processing Pipeline ce2747e5015c7e856e938d40df5e310a https://www.encodeproject.org/files/ENCFF266ORV/@@download/ENCFF266ORV.bed.gz hg19 released file validation error, low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance mismatched file status ENCFF044NEB bed narrowPeak optimal idr thresholded peaks ENCSR954WVZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ESRRA-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF486JBY, ENCFF526YPV, ENCFF671MPM 217643 ENCODE Processing Pipeline 513e2c9ea79bc8dcc6bb801f67e6a7b5 https://www.encodeproject.org/files/ENCFF044NEB/@@download/ENCFF044NEB.bed.gz hg19 released mild to moderate bottlenecking ENCFF779HAK bed narrowPeak optimal idr thresholded peaks ENCSR080CST ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-ZNF639-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF286QPO, ENCFF358DXV, ENCFF475IAW 330900 ENCODE Processing Pipeline 8722fa4f64d15c5fcac98cd932aaeed0 https://www.encodeproject.org/files/ENCFF779HAK/@@download/ENCFF779HAK.bed.gz hg19 released missing genetic modification characterization missing control alignments ENCFF651PWG bed narrowPeak optimal idr thresholded peaks ENCSR135ANT ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens NRF1-human DNA False 2016-06-14 ENCODE 1, 3 ENCFF001TDO, ENCFF187EXP, ENCFF444PKI, ENCFF466LLW 120459 ENCODE Processing Pipeline f02c4a616c04a2ab5784f3edd9a3c916 https://www.encodeproject.org/files/ENCFF651PWG/@@download/ENCFF651PWG.bed.gz hg19 released ENCFF492GXZ bed narrowPeak optimal idr thresholded peaks ENCSR508DQA ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOXK2-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF158PJI, ENCFF188GHO, ENCFF451DBC 368132 ENCODE Processing Pipeline 78f64e4354c002e60b1ba43e77ebe73c https://www.encodeproject.org/files/ENCFF492GXZ/@@download/ENCFF492GXZ.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF075PDC bed narrowPeak optimal idr thresholded peaks ENCSR210ZYL ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NBN-human DNA False 2017-05-18 ENCODE 3, 4 ENCFF001TDO, ENCFF084RKF, ENCFF860QPW, ENCFF904SKF 48337 ENCODE Processing Pipeline abda608c14d5e0e618df18420c4dc60b https://www.encodeproject.org/files/ENCFF075PDC/@@download/ENCFF075PDC.bed.gz hg19 released borderline replicate concordance ENCFF188XRD bed narrowPeak optimal idr thresholded peaks ENCSR892DRK ChIP-seq EFO:0001086 A549 cell line Homo sapiens REST-human DNA False 2016-11-23 ENCODE 1, 2 ENCFF001TDO, ENCFF430GOT, ENCFF767OVA, ENCFF819QEC 183739 ENCODE Processing Pipeline 628ccc989464e3745af21f78c7c0831b https://www.encodeproject.org/files/ENCFF188XRD/@@download/ENCFF188XRD.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption ENCFF405RGE bed narrowPeak optimal idr thresholded peaks ENCSR984MDV ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-ZNF24-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF581CAJ, ENCFF722BQJ, ENCFF899PSA 404688 ENCODE Processing Pipeline 6f19ceea45043e71e9e58aef27978f87 https://www.encodeproject.org/files/ENCFF405RGE/@@download/ENCFF405RGE.bed.gz hg19 released missing genetic modification characterization missing control alignments ENCFF735WFO bed narrowPeak optimal idr thresholded peaks ENCSR061DGF ChIP-seq EFO:0007950 GM23338 induced pluripotent stem cell line Homo sapiens NANOG-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF039PBB, ENCFF326RNA, ENCFF967PXA 200875 ENCODE Processing Pipeline 29c10e45fa37cf7416d81f1e6f977d5c https://www.encodeproject.org/files/ENCFF735WFO/@@download/ENCFF735WFO.bed.gz hg19 released borderline replicate concordance, antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF520CSO bed narrowPeak optimal idr thresholded peaks ENCSR862PNL ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens L3MBTL2-human DNA False 2016-11-21 ENCODE 1, 2 ENCFF001TDO, ENCFF394TJZ, ENCFF730CLD, ENCFF836EUO 494230 ENCODE Processing Pipeline 630131dae357dfd7d8bf962892cbc130 https://www.encodeproject.org/files/ENCFF520CSO/@@download/ENCFF520CSO.bed.gz hg19 released mild to moderate bottlenecking ENCFF726VEK bed narrowPeak optimal idr thresholded peaks ENCSR014YCR ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ATF7-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF225TLM, ENCFF640EFU, ENCFF938MOR 702985 ENCODE Processing Pipeline 854d3dcf4854f6b4f25251cadf429439 https://www.encodeproject.org/files/ENCFF726VEK/@@download/ENCFF726VEK.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF213EPU bed narrowPeak optimal idr thresholded peaks ENCSR486IFJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens ESRRA-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF106AUG, ENCFF406YGF, ENCFF619KMH 592333 ENCODE Processing Pipeline bfd05e28fd40d1e2a57b194812d2950e https://www.encodeproject.org/files/ENCFF213EPU/@@download/ENCFF213EPU.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF659WAF bed narrowPeak optimal idr thresholded peaks ENCSR343ELW ChIP-seq EFO:0002067 K562 cell line Homo sapiens LEF1-human DNA False 2016-07-05 ENCODE 3, 4 ENCFF001TDO, ENCFF421AHE, ENCFF506NOD, ENCFF857NTV 338164 ENCODE Processing Pipeline 17a9dcb21ebd4ab5fd04becd0fe896f9 https://www.encodeproject.org/files/ENCFF659WAF/@@download/ENCFF659WAF.bed.gz hg19 released mild to moderate bottlenecking ENCFF166OZW bed narrowPeak optimal idr thresholded peaks ENCSR590KEQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ARNT-human DNA False 2017-11-14 ENCODE 2, 3 ENCFF001TDO, ENCFF076KST, ENCFF120JZJ, ENCFF432CDN 392782 ENCODE Processing Pipeline bc27294f20916f956fe9f163466e61a7 https://www.encodeproject.org/files/ENCFF166OZW/@@download/ENCFF166OZW.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity experiment not submitted to GEO ENCFF144FQA bed narrowPeak optimal idr thresholded peaks ENCSR171FUX ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXK2-human DNA False 2016-04-22 ENCODE 1, 2 ENCFF001TDO, ENCFF076ZSW, ENCFF765WNF, ENCFF834WHV 196025 ENCODE Processing Pipeline 17e7c688b36ce8a85f53635d7fa8324d https://www.encodeproject.org/files/ENCFF144FQA/@@download/ENCFF144FQA.bed.gz hg19 released ENCFF849ZUF bed narrowPeak optimal idr thresholded peaks ENCSR563YDA ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDGF-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF328KFN, ENCFF415ZVO, ENCFF701JMF 214540 ENCODE Processing Pipeline 5889d9be33d5b555b97ac8b885edd835 https://www.encodeproject.org/files/ENCFF849ZUF/@@download/ENCFF849ZUF.bed.gz hg19 released ENCFF676NPW bed narrowPeak optimal idr thresholded peaks ENCSR091JXL ChIP-seq EFO:0002067 K562 cell line Homo sapiens HES1-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF222PPL, ENCFF786MKH, ENCFF860KMP 171892 ENCODE Processing Pipeline b2426299acedb3521638e6d425f68ba5 https://www.encodeproject.org/files/ENCFF676NPW/@@download/ENCFF676NPW.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF904HOD bed narrowPeak optimal idr thresholded peaks ENCSR076EZB ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-KLF9-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF269OXE, ENCFF344BWA, ENCFF621XNB 446663 ENCODE Processing Pipeline 33190e94f5e15116004409a0363b4ac7 https://www.encodeproject.org/files/ENCFF904HOD/@@download/ENCFF904HOD.bed.gz hg19 released low read depth, missing genetic modification characterization missing control alignments ENCFF776XRJ bed narrowPeak optimal idr thresholded peaks ENCSR252QYR ChIP-seq CL:0000182 hepatocyte in vitro differentiated cells Homo sapiens CTCF-human DNA False 2016-11-23 ENCODE 1, 2 ENCFF001TDO, ENCFF345DIK, ENCFF930XLW, ENCFF996USV 797130 ENCODE Processing Pipeline 84d8d7eb11a665074e4b30090ff0197d https://www.encodeproject.org/files/ENCFF776XRJ/@@download/ENCFF776XRJ.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample poor library complexity ENCFF539CKD bed narrowPeak optimal idr thresholded peaks ENCSR542FLV ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZBTB33-human DNA False 2017-11-13 ENCODE 1, 4 ENCFF001TDO, ENCFF038RJE, ENCFF480CCO, ENCFF833YUF 175352 ENCODE Processing Pipeline 7d363f200e0f6652249cddc58feb5f2d https://www.encodeproject.org/files/ENCFF539CKD/@@download/ENCFF539CKD.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance experiment not submitted to GEO ENCFF905VXX bed narrowPeak optimal idr thresholded peaks ENCSR429XTR ChIP-seq EFO:0002067 K562 cell line Homo sapiens TARDBP-human DNA SDS formaldehyde False 2017-02-27 ENCODE 1, 2 ENCFF001TDO, ENCFF368IHM, ENCFF700XRO, ENCFF958WJN 148569 ENCODE Processing Pipeline dc9b0aa9306a30f02136fb2eb7c10c72 https://www.encodeproject.org/files/ENCFF905VXX/@@download/ENCFF905VXX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF095GMM bed narrowPeak optimal idr thresholded peaks ENCSR987MTA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BHLHE40-human DNA False 2017-01-31 ENCODE 4, 5 ENCFF001TDO, ENCFF172YHV, ENCFF468GKJ, ENCFF884ZYH 904897 ENCODE Processing Pipeline c23284256b4100cd845e6f844e468872 https://www.encodeproject.org/files/ENCFF095GMM/@@download/ENCFF095GMM.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth duplicate lane review ENCFF032DEW bed narrowPeak optimal idr thresholded peaks ENCSR243INX ChIP-seq EFO:0002847 PC-9 cell line Homo sapiens CTCF-human DNA False 2017-01-12 ENCODE 1, 2 ENCFF001TDO, ENCFF227KPY, ENCFF399PZK, ENCFF524ADR 1077256 ENCODE Processing Pipeline 2af95dd3b3a987bf9d9c29d4340c0e5b https://www.encodeproject.org/files/ENCFF032DEW/@@download/ENCFF032DEW.bed.gz hg19 released mild to moderate bottlenecking, mixed run types, moderate library complexity, antibody characterized with exemption NTR biosample ENCFF152VMJ bed narrowPeak optimal idr thresholded peaks ENCSR201NQZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTBP1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF066ESG, ENCFF467AZP, ENCFF860LBQ 860855 ENCODE Processing Pipeline 43558d97b59309ab4ef82a6f8566b6ec https://www.encodeproject.org/files/ENCFF152VMJ/@@download/ENCFF152VMJ.bed.gz hg19 released borderline replicate concordance ENCFF614VFL bed narrowPeak optimal idr thresholded peaks ENCSR157CAU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZKSCAN1-human DNA False 2014-07-07 ENCODE 1, 3 ENCFF001TDO, ENCFF312ZWV, ENCFF354CCY, ENCFF893SRK 129340 ENCODE Processing Pipeline 36b24c36febd1db2d5ea0e2fc9789689 https://www.encodeproject.org/files/ENCFF614VFL/@@download/ENCFF614VFL.bed.gz hg19 released low read length, borderline replicate concordance ENCFF411BAO bed narrowPeak optimal idr thresholded peaks ENCSR140DSL ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MAFF-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF145POH, ENCFF492VYK, ENCFF997ZWI 417897 ENCODE Processing Pipeline 93e40b0388115ea73bf792c3d8ac3034 https://www.encodeproject.org/files/ENCFF411BAO/@@download/ENCFF411BAO.bed.gz hg19 released low read length ENCFF085BBF bed narrowPeak optimal idr thresholded peaks ENCSR179SAO ChIP-seq EFO:0002106 A673 cell line Homo sapiens EZH2-human DNA False 2017-11-29 ENCODE 1, 2 ENCFF001TDO, ENCFF155LWQ, ENCFF220SFO, ENCFF396SZC 141143 ENCODE Processing Pipeline 62e8c175705b78fd53128f0862c166eb https://www.encodeproject.org/files/ENCFF085BBF/@@download/ENCFF085BBF.bed.gz hg19 released borderline replicate concordance, low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF761MGJ bed narrowPeak optimal idr thresholded peaks ENCSR681NOM ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CEBPB-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF017STY, ENCFF284OML, ENCFF300RLB 41700 ENCODE Processing Pipeline 380214c27906f67ff28dec054d68900a https://www.encodeproject.org/files/ENCFF761MGJ/@@download/ENCFF761MGJ.bed.gz hg19 released low read length, low read depth ENCFF246VJH bed narrowPeak optimal idr thresholded peaks ENCSR377BLZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens GTF2F1-human DNA SDS formaldehyde False 2018-01-16 ENCODE 1, 2 ENCFF001TDO, ENCFF498CHM, ENCFF559OHC, ENCFF583UDD 263665 ENCODE Processing Pipeline 73c53958a16e09e0c2ba93843f2da5c4 https://www.encodeproject.org/files/ENCFF246VJH/@@download/ENCFF246VJH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF601XVA bed narrowPeak optimal idr thresholded peaks ENCSR785OKZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RB1-human DNA formaldehyde False 2017-06-07 ENCODE 3, 4 ENCFF001TDO, ENCFF436OTJ, ENCFF452IKX, ENCFF936FBJ 363397 ENCODE Processing Pipeline 04fd5d92531b46908c2f3bf60b199d9a https://www.encodeproject.org/files/ENCFF601XVA/@@download/ENCFF601XVA.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance ENCFF620ZDF bed narrowPeak optimal idr thresholded peaks ENCSR859BMR ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-KLF1-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF045DDN, ENCFF177PBO, ENCFF875YEH 690446 ENCODE Processing Pipeline 2698efb354794c0218e90f40df413017 https://www.encodeproject.org/files/ENCFF620ZDF/@@download/ENCFF620ZDF.bed.gz hg19 released missing genetic modification characterization missing control alignments ENCFF492DZG bed narrowPeak optimal idr thresholded peaks ENCSR288IJC ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MAZ-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF184RLT, ENCFF386ILV, ENCFF917ALR 364883 ENCODE Processing Pipeline 1671a4b78c9af2be9439811695455aab https://www.encodeproject.org/files/ENCFF492DZG/@@download/ENCFF492DZG.bed.gz hg19 released antibody characterized with exemption ENCFF754GUT bed narrowPeak optimal idr thresholded peaks ENCSR563FBT ChIP-seq EFO:0001086 A549 cell line Homo sapiens USF2-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF228YLF, ENCFF664JOM, ENCFF735LLC 215763 ENCODE Processing Pipeline f6f7b983fea0068328111da329526b42 https://www.encodeproject.org/files/ENCFF754GUT/@@download/ENCFF754GUT.bed.gz hg19 released antibody characterized with exemption ENCFF980KSV bed narrowPeak optimal idr thresholded peaks ENCSR861JUQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens FOXK2-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF014VXF, ENCFF348PZF, ENCFF870DSA 101906 ENCODE Processing Pipeline ceed3be232cda7bc789bc4f322683f0f https://www.encodeproject.org/files/ENCFF980KSV/@@download/ENCFF980KSV.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF756HSC bed narrowPeak optimal idr thresholded peaks ENCSR584ATA ChIP-seq EFO:0006710 OCI-LY3 cell line Homo sapiens EZH2phosphoT487-human DNA False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF796TTQ, ENCFF824PBX, ENCFF895NJW 33287 ENCODE Processing Pipeline 26be33f99880f04312294e96795f82df https://www.encodeproject.org/files/ENCFF756HSC/@@download/ENCFF756HSC.bed.gz hg19 released mixed run types, low read depth, antibody characterized with exemption biological replicates with identical biosample, NTR biosample, experiment not submitted to GEO ENCFF507MGL bed narrowPeak optimal idr thresholded peaks ENCSR155KHM ChIP-seq EFO:0002067 K562 cell line Homo sapiens ARNT-human DNA False 2016-04-21 ENCODE 1, 2 ENCFF001TDO, ENCFF011UZZ, ENCFF071HZE, ENCFF652WXC 214239 ENCODE Processing Pipeline 5840c9b0b65a89375f82d3cdf94ec1f5 https://www.encodeproject.org/files/ENCFF507MGL/@@download/ENCFF507MGL.bed.gz hg19 released mild to moderate bottlenecking ENCFF343ULZ bed narrowPeak optimal idr thresholded peaks ENCSR866QPZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ATF7-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF015TCM, ENCFF391ODX, ENCFF998CHH 434730 ENCODE Processing Pipeline 4ad000f92723a9df7fab2b70ff4cf1c9 https://www.encodeproject.org/files/ENCFF343ULZ/@@download/ENCFF343ULZ.bed.gz hg19 released mild to moderate bottlenecking, low read depth, antibody characterized with exemption ENCFF144FCI bed narrowPeak optimal idr thresholded peaks ENCSR900XDB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZFP36-human DNA False 2014-07-07 ENCODE 4, 5 ENCFF001TDO, ENCFF380MCV, ENCFF527IRJ, ENCFF772RKI 175071 ENCODE Processing Pipeline 725a70663ca7828abe2e411b97c0330b https://www.encodeproject.org/files/ENCFF144FCI/@@download/ENCFF144FCI.bed.gz hg19 released low read length, mild to moderate bottlenecking experiment not submitted to GEO partially characterized antibody ENCFF355OQM bed narrowPeak optimal idr thresholded peaks ENCSR066BZZ ChIP-seq CL:0000103 bipolar neuron in vitro differentiated cells Homo sapiens doxycycline hyclate 0.5 μg/mL 4 day CTCF-human DNA False 2016-11-24 ENCODE 1, 2 ENCFF001TDO, ENCFF282QPK, ENCFF566IFZ, ENCFF752PSY 1382660 ENCODE Processing Pipeline aa33c900320825756bfd377ef566f12e https://www.encodeproject.org/files/ENCFF355OQM/@@download/ENCFF355OQM.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption NTR biosample ENCFF424KTS bed narrowPeak optimal idr thresholded peaks ENCSR101FJS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TBL1XR1-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF342PPK, ENCFF824GTA, ENCFF924XCI 184822 ENCODE Processing Pipeline 15651a1c0a92804f9536eab9314b760b https://www.encodeproject.org/files/ENCFF424KTS/@@download/ENCFF424KTS.bed.gz hg19 released low read length, borderline replicate concordance, low read depth experiment not submitted to GEO partially characterized antibody ENCFF314ULQ bed narrowPeak optimal idr thresholded peaks ENCSR530XQI ChIP-seq EFO:0002067 K562 cell line Homo sapiens L3MBTL2-human DNA False 2016-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF471MPD, ENCFF706LNT, ENCFF875ISD 1006532 ENCODE Processing Pipeline 807407007c047f1cd624d59e5aff4373 https://www.encodeproject.org/files/ENCFF314ULQ/@@download/ENCFF314ULQ.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF490ZAU bed narrowPeak optimal idr thresholded peaks ENCSR825MZS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TAF15-human DNA SDS formaldehyde False 2018-01-16 ENCODE 1, 2 ENCFF001TDO, ENCFF137VXT, ENCFF762IGQ, ENCFF853BNC 346126 ENCODE Processing Pipeline 1e317e05556ff5fd386ff3b050195ef3 https://www.encodeproject.org/files/ENCFF490ZAU/@@download/ENCFF490ZAU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF221ZIG bed narrowPeak optimal idr thresholded peaks ENCSR131FFJ ChIP-seq EFO:0005723 GM23248 cell line Homo sapiens EZH2-human DNA False 2018-03-09 ENCODE 1, 2 ENCFF001TDO, ENCFF486RTH, ENCFF661PVV, ENCFF878CWL 139515 ENCODE Processing Pipeline 41cd894388403b3786f034d4ed8bfea6 https://www.encodeproject.org/files/ENCFF221ZIG/@@download/ENCFF221ZIG.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, experiment not submitted to GEO insufficient read depth, poor library complexity, severe bottlenecking ENCFF868QLL bed narrowPeak optimal idr thresholded peaks ENCSR972ZBV ChIP-seq EFO:0002067 K562 cell line Homo sapiens ATF7-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF606UFV, ENCFF611BUY, ENCFF821WIF 855049 ENCODE Processing Pipeline 96c0eed56cbef77b05a368374d122077 https://www.encodeproject.org/files/ENCFF868QLL/@@download/ENCFF868QLL.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF622DUX bed narrowPeak optimal idr thresholded peaks ENCSR000DPP ChIP-seq NTR:0000479 AG09309 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF042OUP, ENCFF299COL, ENCFF437UAR 711204 ENCODE Processing Pipeline 0d3d0dc20ceb418bf2381474049dad66 https://www.encodeproject.org/files/ENCFF622DUX/@@download/ENCFF622DUX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms NTR biosample control insufficient read depth, insufficient read depth missing control alignments ENCFF418WAW bed narrowPeak optimal idr thresholded peaks ENCSR240PRQ ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens CTCF-human DNA see document see document False 2017-10-19 ENCODE 1, 2 ENCFF001TDO, ENCFF222WLA, ENCFF417KAW, ENCFF963ROK 969434 ENCODE Processing Pipeline 3056834266bad8a9c6e898a1b1c33d74 https://www.encodeproject.org/files/ENCFF418WAW/@@download/ENCFF418WAW.bed.gz hg19 released low read length, mixed run types, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF365WFM bed narrowPeak optimal idr thresholded peaks ENCSR697CUP ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens HCFC1-human DNA False 2016-02-16 ENCODE 1, 3 ENCFF001TDO, ENCFF501NKG, ENCFF701BHY, ENCFF938AEH 239330 ENCODE Processing Pipeline 03b8c0259791519294cbf7103dec34a8 https://www.encodeproject.org/files/ENCFF365WFM/@@download/ENCFF365WFM.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF365ICU bed narrowPeak optimal idr thresholded peaks ENCSR611WZO ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens SREBF2-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF039TDK, ENCFF427ZLR, ENCFF969UCK 95703 ENCODE Processing Pipeline 452936171288c14882683e4db423b6c3 https://www.encodeproject.org/files/ENCFF365ICU/@@download/ENCFF365ICU.bed.gz hg19 released mild to moderate bottlenecking ENCFF711OSR bed narrowPeak optimal idr thresholded peaks ENCSR439WAF ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens E4F1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF054XUN, ENCFF471IVB, ENCFF717MTX 110065 ENCODE Processing Pipeline f1f2426bc50072ce5eede047ee65a239 https://www.encodeproject.org/files/ENCFF711OSR/@@download/ENCFF711OSR.bed.gz hg19 released mild to moderate bottlenecking experiment not submitted to GEO partially characterized antibody ENCFF303PMJ bed narrowPeak optimal idr thresholded peaks ENCSR635EXI ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZSCAN29-human DNA False 2017-11-20 ENCODE 1, 3 ENCFF001TDO, ENCFF259GFJ, ENCFF301MWW, ENCFF959BCM 105003 ENCODE Processing Pipeline d1ef6c0a0056c7d72b674fe178969dd2 https://www.encodeproject.org/files/ENCFF303PMJ/@@download/ENCFF303PMJ.bed.gz hg19 released experiment not submitted to GEO ENCFF751DRF bed narrowPeak optimal idr thresholded peaks ENCSR897ZXU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens E2F8-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF093MAU, ENCFF226PXS, ENCFF262ETY 45000 ENCODE Processing Pipeline c3e581d5c27bb0218e2a3c4578ef20bf https://www.encodeproject.org/files/ENCFF751DRF/@@download/ENCFF751DRF.bed.gz hg19 released experiment not submitted to GEO partially characterized antibody ENCFF007ATC bed narrowPeak optimal idr thresholded peaks ENCSR520VTO ChIP-seq EFO:0005907 OCI-LY1 cell line Homo sapiens EZH2-human DNA see document see document False 2017-11-19 ENCODE 1, 2 ENCFF001TDO, ENCFF017WDB, ENCFF419TOT, ENCFF474LJV 3218 ENCODE Processing Pipeline 8ca2251e458ef9a0aea0ba9d03b41b8e https://www.encodeproject.org/files/ENCFF007ATC/@@download/ENCFF007ATC.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, mixed run types, low read depth, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF544NXC bed narrowPeak optimal idr thresholded peaks ENCSR936XTK ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF143-human DNA False 2016-07-28 ENCODE 2, 3 ENCFF001TDO, ENCFF114HTB, ENCFF405WZX, ENCFF648GNP 570474 ENCODE Processing Pipeline b1e487a875b568f4b5945bd06240fbe7 https://www.encodeproject.org/files/ENCFF544NXC/@@download/ENCFF544NXC.bed.gz hg19 released mild to moderate bottlenecking mismatched file status ENCFF757YVY bed narrowPeak optimal idr thresholded peaks ENCSR664OKA ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens ELK1-human DNA False 2016-09-01 ENCODE 1, 2 ENCFF001TDO, ENCFF147QXV, ENCFF306SXM, ENCFF577IGI 11970 ENCODE Processing Pipeline f018341d3a30509fa7fc898006745013 https://www.encodeproject.org/files/ENCFF757YVY/@@download/ENCFF757YVY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity duplicate lane review ENCFF586KIH bed narrowPeak optimal idr thresholded peaks ENCSR000AHD ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF664CSQ, ENCFF762LDF, ENCFF768KKE 916340 ENCODE Processing Pipeline 5a8e504b171a26058efc3a830eef1183 https://www.encodeproject.org/files/ENCFF586KIH/@@download/ENCFF586KIH.bed.gz hg19 released mild to moderate bottlenecking, low read depth ENCFF140MVM bed narrowPeak optimal idr thresholded peaks ENCSR069DPL ChIP-seq NTR:0000711 neural progenitor cell in vitro differentiated cells Homo sapiens EZH2-human DNA False 2017-11-16 ENCODE 1, 2 ENCFF001TDO, ENCFF006UUP, ENCFF024LWI, ENCFF483PBA 443965 ENCODE Processing Pipeline 32b5d01223cb50a1a20a210ec3c20256 https://www.encodeproject.org/files/ENCFF140MVM/@@download/ENCFF140MVM.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF247GZH bed narrowPeak optimal idr thresholded peaks ENCSR072EUE ChIP-seq EFO:0005907 OCI-LY1 cell line Homo sapiens CTCF-human DNA see document see document False 2017-11-13 ENCODE 1, 2 ENCFF001TDO, ENCFF210LCR, ENCFF827ONU, ENCFF990HKP 897307 ENCODE Processing Pipeline 9500ee7049128a297fadb6618bc4d112 https://www.encodeproject.org/files/ENCFF247GZH/@@download/ENCFF247GZH.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity, mixed read lengths, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF985TSH bed narrowPeak optimal idr thresholded peaks ENCSR815ZDS ChIP-seq EFO:0002067 K562 cell line Homo sapiens SREBF1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF554XAI, ENCFF716GBZ, ENCFF826WTJ 53139 ENCODE Processing Pipeline 5d034408cc2d73bb6d706caeaaeeb6ae https://www.encodeproject.org/files/ENCFF985TSH/@@download/ENCFF985TSH.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF312RFN bed narrowPeak optimal idr thresholded peaks ENCSR888XZK ChIP-seq EFO:0002067 K562 cell line Homo sapiens TCF7L2-human DNA False 2016-07-28 ENCODE 1, 2 ENCFF001TDO, ENCFF060XZX, ENCFF274DVQ, ENCFF975NRI 34454 ENCODE Processing Pipeline 0d2abc09baae3bbab2319c87770d5ba6 https://www.encodeproject.org/files/ENCFF312RFN/@@download/ENCFF312RFN.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF884RAO bed narrowPeak optimal idr thresholded peaks ENCSR231ENE ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ARID3A-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF041CMD, ENCFF500TQK, ENCFF749YOZ 28997 ENCODE Processing Pipeline e9107d75716f1b238516c9e39715ad08 https://www.encodeproject.org/files/ENCFF884RAO/@@download/ENCFF884RAO.bed.gz hg19 released borderline replicate concordance ENCFF015PGM bed narrowPeak optimal idr thresholded peaks ENCSR788XNX ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens RFX1-human DNA False 2016-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF270NHR, ENCFF633FJC, ENCFF736XAR 253341 ENCODE Processing Pipeline 1ab6521ee737225dbeff8ca8348955fb https://www.encodeproject.org/files/ENCFF015PGM/@@download/ENCFF015PGM.bed.gz hg19 released low read depth ENCFF318QLK bed narrowPeak optimal idr thresholded peaks ENCSR882ICT ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens ZNF384-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF407DGA, ENCFF930CXT, ENCFF943FOK 324419 ENCODE Processing Pipeline a9c5e13520aed738df7f24f3f65c52fe https://www.encodeproject.org/files/ENCFF318QLK/@@download/ENCFF318QLK.bed.gz hg19 released ENCFF287ORE bed narrowPeak optimal idr thresholded peaks ENCSR042TWZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens SNIP1-human DNA False 2017-06-23 ENCODE 1, 2 ENCFF001TDO, ENCFF012TME, ENCFF689XKH, ENCFF749UEV 68038 ENCODE Processing Pipeline 82dd3d27f3266ae674d6b855a13c6937 https://www.encodeproject.org/files/ENCFF287ORE/@@download/ENCFF287ORE.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity ENCFF178LCE bed narrowPeak optimal idr thresholded peaks ENCSR912ATU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF217-human DNA False 2017-11-13 ENCODE 2, 3 ENCFF001TDO, ENCFF176ZIJ, ENCFF740DFA, ENCFF988SMP 59384 ENCODE Processing Pipeline 615eeee00b09b2d3f598326eb3bee61d https://www.encodeproject.org/files/ENCFF178LCE/@@download/ENCFF178LCE.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption experiment not submitted to GEO ENCFF344OJI bed narrowPeak optimal idr thresholded peaks ENCSR205SKQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens YBX1-human DNA False 2016-08-24 ENCODE 1, 2 ENCFF001TDO, ENCFF009QEI, ENCFF015RED, ENCFF019TVN 44947 ENCODE Processing Pipeline 8f76cd4eaefe9893f5ed8affc6e9a2ad https://www.encodeproject.org/files/ENCFF344OJI/@@download/ENCFF344OJI.bed.gz hg19 released file validation error, borderline replicate concordance, antibody characterized with exemption mismatched file status ENCFF935HIG bed narrowPeak optimal idr thresholded peaks ENCSR145XQO ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens HDGF-human DNA False 2016-08-24 ENCODE 1, 2 ENCFF001TDO, ENCFF432SFP, ENCFF637CIX, ENCFF816GZA 401608 ENCODE Processing Pipeline 10e3149096e5eb728da6251a011656f6 https://www.encodeproject.org/files/ENCFF935HIG/@@download/ENCFF935HIG.bed.gz hg19 released file validation error, antibody characterized with exemption mismatched file status ENCFF359IPV bed narrowPeak optimal idr thresholded peaks ENCSR124AIG ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens FOS-human DNA False 2016-12-19 ENCODE 1, 2 ENCFF001TDO, ENCFF332EWZ, ENCFF522TKF, ENCFF714YWI 579404 ENCODE Processing Pipeline 8fe42a8e0c96a42da9a055e03e58aed6 https://www.encodeproject.org/files/ENCFF359IPV/@@download/ENCFF359IPV.bed.gz hg19 released low read length, low read depth duplicate lane review ENCFF581ZZT bed narrowPeak optimal idr thresholded peaks ENCSR742TMU ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF282-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF313WJM, ENCFF603AEE, ENCFF802MWF 244445 ENCODE Processing Pipeline 1ee0c43847b45d2db7e83b4bc1c076d2 https://www.encodeproject.org/files/ENCFF581ZZT/@@download/ENCFF581ZZT.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity experiment not submitted to GEO partially characterized antibody ENCFF550UEU bed narrowPeak optimal idr thresholded peaks ENCSR760UKJ ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens ARNT-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF121FBN, ENCFF139FWO, ENCFF715GDR 98682 ENCODE Processing Pipeline 813259a064946656fcfdc88f1bede48e https://www.encodeproject.org/files/ENCFF550UEU/@@download/ENCFF550UEU.bed.gz hg19 released mild to moderate bottlenecking ENCFF444QJT bed narrowPeak optimal idr thresholded peaks ENCSR565XSL ChIP-seq EFO:0006711 OCI-LY7 cell line Homo sapiens EZH2phosphoT487-human DNA see document see document False 2018-02-06 ENCODE 1, 2 ENCFF001TDO, ENCFF283OGT, ENCFF502WVO, ENCFF750MDG 24131 ENCODE Processing Pipeline e9c7996dbbdf5f9133abc392aadbdfe7 https://www.encodeproject.org/files/ENCFF444QJT/@@download/ENCFF444QJT.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, mixed run types, low read depth, antibody characterized with exemption, mixed read lengths NTR biosample, experiment not submitted to GEO ENCFF304IDM bed narrowPeak optimal idr thresholded peaks ENCSR265ARE ChIP-seq EFO:0007752 VCaP cell line Homo sapiens CTCF-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF247RAX, ENCFF514JGP, ENCFF536CTG 1543624 ENCODE Processing Pipeline 56d93fec54a90ac5c5269b5284cc2f20 https://www.encodeproject.org/files/ENCFF304IDM/@@download/ENCFF304IDM.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF561WNI bed narrowPeak optimal idr thresholded peaks ENCSR197ALX ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDGF-human DNA False 2016-08-05 ENCODE 1, 2 ENCFF001TDO, ENCFF264KUV, ENCFF385LTD, ENCFF409HKO 176911 ENCODE Processing Pipeline 938fcbd1e3573ad84cdb46925b19eb89 https://www.encodeproject.org/files/ENCFF561WNI/@@download/ENCFF561WNI.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF516AJC bed narrowPeak optimal idr thresholded peaks ENCSR597VGC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ETV6-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF831JVY, ENCFF862QRJ, ENCFF959JZX 74606 ENCODE Processing Pipeline 316374d55e9babf8e309648be088e6f9 https://www.encodeproject.org/files/ENCFF516AJC/@@download/ENCFF516AJC.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity ENCFF451RKK bed narrowPeak optimal idr thresholded peaks ENCSR557JTZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GTF2F1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF331EWI, ENCFF376IUM, ENCFF601FJF 214449 ENCODE Processing Pipeline 2f9f6a2c05c6da3570536da4a30e062d https://www.encodeproject.org/files/ENCFF451RKK/@@download/ENCFF451RKK.bed.gz hg19 released ENCFF282AEY bed narrowPeak optimal idr thresholded peaks ENCSR623KNM ChIP-seq EFO:0001086 A549 cell line Homo sapiens ELK1-human DNA False 2014-07-07 ENCODE 1, 3 ENCFF001TDO, ENCFF044AVI, ENCFF056BGC, ENCFF294MMU 9345 ENCODE Processing Pipeline 406629fca7d1601a984475d602c7c8cb https://www.encodeproject.org/files/ENCFF282AEY/@@download/ENCFF282AEY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance duplicate lane review ENCFF503AZK bed narrowPeak optimal idr thresholded peaks ENCSR337NWW ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens HDAC2-human DNA False 2016-10-14 ENCODE 1, 2 ENCFF001TDO, ENCFF514KXZ, ENCFF686QQS, ENCFF973BDU 122502 ENCODE Processing Pipeline 524e5189e3cc154582971252084975a0 https://www.encodeproject.org/files/ENCFF503AZK/@@download/ENCFF503AZK.bed.gz hg19 released ENCFF168INE bed narrowPeak optimal idr thresholded peaks ENCSR168SMX ChIP-seq UBERON:0002107 liver tissue Homo sapiens NR2F2-human DNA False 2016-08-18 ENCODE 1, 2 ENCFF001TDO, ENCFF411FEE, ENCFF491JFL, ENCFF615HHV 690741 ENCODE Processing Pipeline 75a88e99090b799ce8034d216030b7e7 https://www.encodeproject.org/files/ENCFF168INE/@@download/ENCFF168INE.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF948TXN bed narrowPeak optimal idr thresholded peaks ENCSR077DKV ChIP-seq EFO:0002067 K562 cell line Homo sapiens CREM-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF045SMN, ENCFF357OAA, ENCFF477IXW 627991 ENCODE Processing Pipeline faf8f9d6ef509ef17dd410cd21d30238 https://www.encodeproject.org/files/ENCFF948TXN/@@download/ENCFF948TXN.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF990CFV bed narrowPeak optimal idr thresholded peaks ENCSR364SNE ChIP-seq EFO:0002067 K562 cell line Homo sapiens POU5F1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF272EQO, ENCFF705MDG, ENCFF768INF 41921 ENCODE Processing Pipeline 8be2419d12baba94256451bb4acfde78 https://www.encodeproject.org/files/ENCFF990CFV/@@download/ENCFF990CFV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance experiment not submitted to GEO partially characterized antibody ENCFF651LIG bed narrowPeak optimal idr thresholded peaks ENCSR352QSB ChIP-seq UBERON:0002107 liver tissue Homo sapiens RXRA-human DNA False 2017-12-01 ENCODE 1, 2 ENCFF001TDO, ENCFF020HWP, ENCFF328XQD, ENCFF458DFL 950321 ENCODE Processing Pipeline c598205029cccfb7ff103ac57aaddb1e https://www.encodeproject.org/files/ENCFF651LIG/@@download/ENCFF651LIG.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF127RVQ bed narrowPeak optimal idr thresholded peaks ENCSR897JAS ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CREB1-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF351PGN, ENCFF521INM, ENCFF634HLA 881747 ENCODE Processing Pipeline 2f0a214c3caca2c724991bc88dc1434a https://www.encodeproject.org/files/ENCFF127RVQ/@@download/ENCFF127RVQ.bed.gz hg19 released ENCFF353QLW bed narrowPeak optimal idr thresholded peaks ENCSR449UFF ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZKSCAN1-human DNA False 2016-06-14 ENCODE 3, 4 ENCFF001TDO, ENCFF013VWS, ENCFF216ONL, ENCFF387UKV 117342 ENCODE Processing Pipeline fa969ad37ed6d708c5126ca4cbe28e79 https://www.encodeproject.org/files/ENCFF353QLW/@@download/ENCFF353QLW.bed.gz hg19 released ENCFF150TBK bed narrowPeak optimal idr thresholded peaks ENCSR066TET ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens RFX1-human DNA False 2016-06-23 ENCODE 1, 3 ENCFF001TDO, ENCFF128GZH, ENCFF367XOV, ENCFF588ODL 483003 ENCODE Processing Pipeline 3b7244abb3c710105e4641632bb37970 https://www.encodeproject.org/files/ENCFF150TBK/@@download/ENCFF150TBK.bed.gz hg19 released mild to moderate bottlenecking ENCFF902IMW bed narrowPeak optimal idr thresholded peaks ENCSR109ODF ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens HES1-human DNA False 2017-04-14 ENCODE 1, 2 ENCFF001TDO, ENCFF609EET, ENCFF779NYR, ENCFF794UGE 92144 ENCODE Processing Pipeline 45232ad38904dc1dbab3a90de46e8176 https://www.encodeproject.org/files/ENCFF902IMW/@@download/ENCFF902IMW.bed.gz hg19 released ENCFF708GMO bed narrowPeak optimal idr thresholded peaks ENCSR230ZWH ChIP-seq UBERON:0002107 liver tissue Homo sapiens RAD21-human DNA False 2016-10-12 ENCODE 1, 2 ENCFF001TDO, ENCFF624XKD, ENCFF950LOX, ENCFF974XKH 1336347 ENCODE Processing Pipeline 7e9fff1df0984cd791bec85be62f671a https://www.encodeproject.org/files/ENCFF708GMO/@@download/ENCFF708GMO.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF814REB bed narrowPeak optimal idr thresholded peaks ENCSR009TKN ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens RCOR1-human DNA False 2017-06-15 ENCODE 1, 2 ENCFF001TDO, ENCFF031DVG, ENCFF310CYQ, ENCFF479KRR 527913 ENCODE Processing Pipeline 02e8d555302bf4688d6bf86a850b6e8d https://www.encodeproject.org/files/ENCFF814REB/@@download/ENCFF814REB.bed.gz hg19 released low read length, antibody characterized with exemption ENCFF530ZTE bed narrowPeak optimal idr thresholded peaks ENCSR541WQI ChIP-seq EFO:0001086 A549 cell line Homo sapiens MAFK-human DNA False 2014-07-07 ENCODE 2, 3 ENCFF001TDO, ENCFF171KTF, ENCFF433MKF, ENCFF973PJK 1217890 ENCODE Processing Pipeline 2cb07e62a7925de227e413eedd005c61 https://www.encodeproject.org/files/ENCFF530ZTE/@@download/ENCFF530ZTE.bed.gz hg19 released experiment not submitted to GEO partially characterized antibody ENCFF168HHB bed narrowPeak optimal idr thresholded peaks ENCSR882ZTS ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens eGFP-ZBTB11-human DNA formaldehyde False 2016-10-07 ENCODE 1, 2 ENCFF001TDO, ENCFF125NRW, ENCFF469FSE, ENCFF541CCM 431630 ENCODE Processing Pipeline fabd7ac2458cd379262c7fb71586ee75 https://www.encodeproject.org/files/ENCFF168HHB/@@download/ENCFF168HHB.bed.gz hg19 released low read depth, missing genetic modification characterization missing control alignments ENCFF924XFS bed narrowPeak optimal idr thresholded peaks ENCSR634OAQ ChIP-seq EFO:0001221 NCI-H929 cell line Homo sapiens CTCF-human DNA False 2017-11-29 ENCODE 1, 2 ENCFF001TDO, ENCFF086DEW, ENCFF750EJJ, ENCFF848FMM 1016167 ENCODE Processing Pipeline 18e6e79e3172d18987ed0ed4bcf0426a https://www.encodeproject.org/files/ENCFF924XFS/@@download/ENCFF924XFS.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, experiment not submitted to GEO insufficient read depth, poor library complexity, severe bottlenecking ENCFF403SBB bed narrowPeak optimal idr thresholded peaks ENCSR541AMF ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens CTCF-human DNA False 2017-11-13 ENCODE 1, 2 ENCFF001TDO, ENCFF040XUI, ENCFF399EZO, ENCFF519MIS 1050603 ENCODE Processing Pipeline 0e395f73816b021cc996d73f8b1fa49c https://www.encodeproject.org/files/ENCFF403SBB/@@download/ENCFF403SBB.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption NTR biosample, experiment not submitted to GEO ENCFF503SZB bed narrowPeak optimal idr thresholded peaks ENCSR422ZAO ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens IRF3-human DNA False 2016-11-10 ENCODE 2, 3 ENCFF001TDO, ENCFF253SCW, ENCFF360UWJ, ENCFF910MED 18928 ENCODE Processing Pipeline 2aea4dec6d18664385af8d5c9fd590ef https://www.encodeproject.org/files/ENCFF503SZB/@@download/ENCFF503SZB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance ENCFF236XBR bed narrowPeak optimal idr thresholded peaks ENCSR350ORK ChIP-seq UBERON:0002107 liver tissue Homo sapiens GABPA-human DNA False 2016-09-09 ENCODE 1, 2 ENCFF001TDO, ENCFF030PHB, ENCFF314VOK, ENCFF808RKL 106579 ENCODE Processing Pipeline 738397904efa4a1ce7b50f6bca1fb8ef https://www.encodeproject.org/files/ENCFF236XBR/@@download/ENCFF236XBR.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption biological replicates with identical biosample ENCFF002CUX bed narrowPeak optimal idr thresholded peaks ENCSR000EVQ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TCF7L2-human DNA see document see document False 2011-10-29 ENCODE 66265 ENCODE Consortium Analysis Working Group 48217ad1de947d3aa04bab64adba7682 https://www.encodeproject.org/files/ENCFF002CUX/@@download/ENCFF002CUX.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF471HCD bed narrowPeak optimal idr thresholded peaks ENCSR000BQI ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CEBPB-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF073ACH, ENCFF721KHE, ENCFF774DWR 315269 ENCODE Processing Pipeline 9811f9d239aa6af3db6a129dcb21b892 https://www.encodeproject.org/files/ENCFF471HCD/@@download/ENCFF471HCD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking ENCFF002CVA bed narrowPeak optimal idr thresholded peaks ENCSR000EVR ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZNF274-human DNA see document see document False 2011-10-29 ENCODE 6190 ENCODE Consortium Analysis Working Group 6d6e5c16bf06e488b8933b0b01da6aee https://www.encodeproject.org/files/ENCFF002CVA/@@download/ENCFF002CVA.bed.gz hg19 released inconsistent platforms biological replicates with identical biosample, missing derived_from insufficient read length ENCFF394CWJ bed narrowPeak optimal idr thresholded peaks ENCSR000BHC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZBTB33-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF141WKX, ENCFF372FLW, ENCFF891ZCM 44775 ENCODE Processing Pipeline 1e1ef221679ba28140cc4103b3ab4bb6 https://www.encodeproject.org/files/ENCFF394CWJ/@@download/ENCFF394CWJ.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF939TZS bed narrowPeak optimal idr thresholded peaks ENCSR897MMC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens JUNB-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF236WSQ, ENCFF294GPL, ENCFF332JOV 594939 ENCODE Processing Pipeline 9d4f96a2a04e052aa45a02e3702c33d5 https://www.encodeproject.org/files/ENCFF939TZS/@@download/ENCFF939TZS.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption ENCFF311LEU bed narrowPeak optimal idr thresholded peaks ENCSR518WPL ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NR2F6-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF289JSG, ENCFF524UVY, ENCFF649MCA 533877 ENCODE Processing Pipeline ecc965b347f5de0a0f97d0a66178b5ab https://www.encodeproject.org/files/ENCFF311LEU/@@download/ENCFF311LEU.bed.gz hg19 released antibody characterized with exemption ENCFF223YXP bed narrowPeak optimal idr thresholded peaks ENCSR997GPO ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens NFRKB-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF026UVT, ENCFF079EBS, ENCFF327WVX 45043 ENCODE Processing Pipeline 7759e7359a29237473e4bdd33e0ea03e https://www.encodeproject.org/files/ENCFF223YXP/@@download/ENCFF223YXP.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity ENCFF266GGD bed narrowPeak optimal idr thresholded peaks ENCSR000DTI ChIP-seq CL:0000746 cardiac muscle cell primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF504WUQ, ENCFF574BPV, ENCFF883SBZ 763849 ENCODE Processing Pipeline 0676fa28175caf0322d3a91f2a8ff9f1 https://www.encodeproject.org/files/ENCFF266GGD/@@download/ENCFF266GGD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF807JAC bed narrowPeak optimal idr thresholded peaks ENCSR000DOZ ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens ethanol 0.01 percent 36.0 hour STAT3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF113OOA, ENCFF487XXM, ENCFF715ZPN 254705 ENCODE Processing Pipeline a129bf26832d975432ee1772843b584d https://www.encodeproject.org/files/ENCFF807JAC/@@download/ENCFF807JAC.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, missing genetic modification characterization, low read depth biological replicates with identical biosample insufficient read depth, severe bottlenecking ENCFF997RPK bed narrowPeak optimal idr thresholded peaks ENCSR551ZDZ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MTA2-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF512TAK, ENCFF665QYO, ENCFF827YDE 21178 ENCODE Processing Pipeline 5327f9e036270e1e5ae60827f370090e https://www.encodeproject.org/files/ENCFF997RPK/@@download/ENCFF997RPK.bed.gz hg19 released borderline replicate concordance ENCFF140ARE bed narrowPeak optimal idr thresholded peaks ENCSR000BNJ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens HNF4G-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF540FQF, ENCFF600JKB, ENCFF608NEP 417895 ENCODE Processing Pipeline 361cfa119c4ac6576c821f2a7dfb483f https://www.encodeproject.org/files/ENCFF140ARE/@@download/ENCFF140ARE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample missing control alignments ENCFF226MQR bed narrowPeak optimal idr thresholded peaks ENCSR000DNC ChIP-seq CL:0000312 keratinocyte primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF680MAX, ENCFF705JDO, ENCFF974JVU 777450 ENCODE Processing Pipeline 88ccad5203a63876e6a75b360b38c092 https://www.encodeproject.org/files/ENCFF226MQR/@@download/ENCFF226MQR.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF242IWJ bed narrowPeak optimal idr thresholded peaks ENCSR189TRZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens TCF12-human DNA False 2016-07-08 ENCODE 1, 2 ENCFF001TDO, ENCFF436EEZ, ENCFF627NVL, ENCFF777QKF 294099 ENCODE Processing Pipeline a3a1e5f8f633db2836973205f624314e https://www.encodeproject.org/files/ENCFF242IWJ/@@download/ENCFF242IWJ.bed.gz hg19 released antibody characterized with exemption ENCFF302XID bed narrowPeak optimal idr thresholded peaks ENCSR000BHB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens EP300-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF043OJL, ENCFF804LKJ, ENCFF901YUN 74253 ENCODE Processing Pipeline 86772eabea3fb88597077cba207fc9b3 https://www.encodeproject.org/files/ENCFF302XID/@@download/ENCFF302XID.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF723RSX bed narrowPeak optimal idr thresholded peaks ENCSR051OUX ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFATC3-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF596YYO, ENCFF607MDM, ENCFF631AZA 249584 ENCODE Processing Pipeline d4f82f8346e6cfaeeea5dffc52df893e https://www.encodeproject.org/files/ENCFF723RSX/@@download/ENCFF723RSX.bed.gz hg19 released mild to moderate bottlenecking experiment not submitted to GEO partially characterized antibody ENCFF434QZL bed narrowPeak optimal idr thresholded peaks ENCSR331GDC ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZBTB11-human DNA False 2016-06-28 ENCODE 1, 2 ENCFF001TDO, ENCFF416FBH, ENCFF429ZJG, ENCFF929FJI 128593 ENCODE Processing Pipeline 4f90e8cc9263cacf63e92bbbf564133f https://www.encodeproject.org/files/ENCFF434QZL/@@download/ENCFF434QZL.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity, antibody characterized with exemption ENCFF065UFF bed narrowPeak optimal idr thresholded peaks ENCSR391JII ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens RCOR1-human DNA False 2016-06-14 ENCODE 3, 4 ENCFF001TDO, ENCFF804UPE, ENCFF833DXW, ENCFF836PMF 168014 ENCODE Processing Pipeline d14e3ffe1f613e32c10a0348cc8affca https://www.encodeproject.org/files/ENCFF065UFF/@@download/ENCFF065UFF.bed.gz hg19 released low read depth ENCFF970LCB bed narrowPeak optimal idr thresholded peaks ENCSR000EGZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens MXI1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF400DMX, ENCFF408TRC, ENCFF492QMD 161913 ENCODE Processing Pipeline 5fde622a545fc7d9f4edabddd920274c https://www.encodeproject.org/files/ENCFF970LCB/@@download/ENCFF970LCB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF141SAU bed narrowPeak optimal idr thresholded peaks ENCSR000DZL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF143-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF046WGV, ENCFF420LVZ, ENCFF704WHY 660604 ENCODE Processing Pipeline 8b9eb2c39e56a1197433faf476328b10 https://www.encodeproject.org/files/ENCFF141SAU/@@download/ENCFF141SAU.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample control insufficient read depth, insufficient replicate concordance ENCFF002CPA bed narrowPeak optimal idr thresholded peaks ENCSR000EAG ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens tumor necrosis factor 25 ng/mL 6 hour RELA-human DNA see document see document False 2012-05-14 ENCODE 414083 ENCODE Consortium Analysis Working Group 536e19e1527ff5f05e1cbf59582972ff https://www.encodeproject.org/files/ENCFF002CPA/@@download/ENCFF002CPA.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF667HLC bed narrowPeak optimal idr thresholded peaks ENCSR000BMG ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDAC2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF246ENE, ENCFF336UZW, ENCFF735NAF 160465 ENCODE Processing Pipeline ee3222ea4ba9e0e28d04252bf3caeb15 https://www.encodeproject.org/files/ENCFF667HLC/@@download/ENCFF667HLC.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking biological replicates with identical biosample poor library complexity, severe bottlenecking extremely low read depth ENCFF747LKL bed narrowPeak optimal idr thresholded peaks ENCSR000BPF ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour TAF1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF371XXQ, ENCFF515ZED, ENCFF606JSI 306040 ENCODE Processing Pipeline be3c3a4fe3dfd0512da67a296562eff7 https://www.encodeproject.org/files/ENCFF747LKL/@@download/ENCFF747LKL.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance biological replicates with identical biosample ENCFF639NGJ bed narrowPeak optimal idr thresholded peaks ENCSR000BPZ ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour ZBTB33-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF213KTM, ENCFF327NKC, ENCFF903RWE 201332 ENCODE Processing Pipeline fa24c935ecf2f82e6f2a303a812a5730 https://www.encodeproject.org/files/ENCFF639NGJ/@@download/ENCFF639NGJ.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF139DOR bed narrowPeak optimal idr thresholded peaks ENCSR000DVI ChIP-seq CL:0002586 retinal pigment epithelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF412BGE, ENCFF647XYZ, ENCFF695UND 908206 ENCODE Processing Pipeline 0a252ead988d04608f92e283a28c1b6c https://www.encodeproject.org/files/ENCFF139DOR/@@download/ENCFF139DOR.bed.gz hg19 released control low read depth, low read length, low read depth, inconsistent platforms ENCFF569IGP bed narrowPeak optimal idr thresholded peaks ENCSR000EBY ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens MYC-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF164IAN, ENCFF241JSX, ENCFF808TOG 118663 ENCODE Processing Pipeline c21c11458242075faf796af2b64d9804 https://www.encodeproject.org/files/ENCFF569IGP/@@download/ENCFF569IGP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF282QFS bed narrowPeak optimal idr thresholded peaks ENCSR000DUM ChIP-seq EFO:0005710 HFF-Myc cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF211MMB, ENCFF683OHM, ENCFF777FSS 658629 ENCODE Processing Pipeline 5cb966acd351fac7cc8466d60a973372 https://www.encodeproject.org/files/ENCFF282QFS/@@download/ENCFF282QFS.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking missing control alignments ENCFF781PAL bed narrowPeak optimal idr thresholded peaks ENCSR000BOZ ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens REST-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF046BKR, ENCFF376SMA, ENCFF546CXR 296216 ENCODE Processing Pipeline 49f87a41db2a31840fd1bfc3d95f27f6 https://www.encodeproject.org/files/ENCFF781PAL/@@download/ENCFF781PAL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF072UEX bed narrowPeak optimal idr thresholded peaks ENCSR000BLS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RAD21-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF020QWB, ENCFF374LID, ENCFF415ZQD 944041 ENCODE Processing Pipeline 1ff2fbb867b1a9a4b26928036292ae06 https://www.encodeproject.org/files/ENCFF072UEX/@@download/ENCFF072UEX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF495MHZ bed narrowPeak optimal idr thresholded peaks ENCSR000FCC ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFE2-human DNA see document see document False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF552ZAY, ENCFF803FZY, ENCFF813HVG 486318 ENCODE Processing Pipeline 7a79922b588af54d6245ba1711aac16f https://www.encodeproject.org/files/ENCFF495MHZ/@@download/ENCFF495MHZ.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF686VJY bed narrowPeak optimal idr thresholded peaks ENCSR000BKD ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF052MDZ, ENCFF535RGW, ENCFF654AYS 425021 ENCODE Processing Pipeline 528631c3a11fa1a1f12c9340d582e94c https://www.encodeproject.org/files/ENCFF686VJY/@@download/ENCFF686VJY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF668VNS bed narrowPeak optimal idr thresholded peaks ENCSR000EUP ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens MAX-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF056RFC, ENCFF566JIH, ENCFF667ZFL 94566 ENCODE Processing Pipeline d5e88944c656337613f322a78d3b9172 https://www.encodeproject.org/files/ENCFF668VNS/@@download/ENCFF668VNS.bed.gz hg19 released borderline replicate concordance biological replicates with identical biosample insufficient read length extremely low read depth ENCFF699ZII bed narrowPeak optimal idr thresholded peaks ENCSR429QPP ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOXM1-human DNA False 2017-01-27 ENCODE 1, 2 ENCFF001TDO, ENCFF804EPQ, ENCFF805KEB, ENCFF847FHY 287070 ENCODE Processing Pipeline 4775f57db3e59a973c0c857c17c0de9b https://www.encodeproject.org/files/ENCFF699ZII/@@download/ENCFF699ZII.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF708LCH bed narrowPeak optimal idr thresholded peaks ENCSR996DUT ChIP-seq EFO:0001086 A549 cell line Homo sapiens JUN-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF155WKH, ENCFF716DUT, ENCFF967FLQ 31888 ENCODE Processing Pipeline 707010bb7e38adb0fb4b076267d2cc41 https://www.encodeproject.org/files/ENCFF708LCH/@@download/ENCFF708LCH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, antibody characterized with exemption ENCFF625SHY bed narrowPeak optimal idr thresholded peaks ENCSR000BNQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BCL3-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF017OSU, ENCFF255RCD, ENCFF306BBY 357177 ENCODE Processing Pipeline 27296c76fc5b23b80e229644883fa76d https://www.encodeproject.org/files/ENCFF625SHY/@@download/ENCFF625SHY.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample insufficient read depth, poor library complexity, severe bottlenecking ENCFF083YCQ bed narrowPeak optimal idr thresholded peaks ENCSR731LHZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens E4F1-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF249GYD, ENCFF713DFK, ENCFF952KDF 454049 ENCODE Processing Pipeline 6f611b81e2e1ca4ecaa174c4c3617412 https://www.encodeproject.org/files/ENCFF083YCQ/@@download/ENCFF083YCQ.bed.gz hg19 released mild to moderate bottlenecking, low read depth experiment not submitted to GEO, out of date analysis partially characterized antibody ENCFF750JOB bed narrowPeak optimal idr thresholded peaks ENCSR000BLB ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens ethanol 0.02 percent 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF010JFS, ENCFF093PHA, ENCFF471HFA 59329 ENCODE Processing Pipeline be4b0fd390fa5e9646dcb71a49dd1488 https://www.encodeproject.org/files/ENCFF750JOB/@@download/ENCFF750JOB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF575FVP bed narrowPeak optimal idr thresholded peaks ENCSR038RXU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens eGFP-GABPA-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF414XXU, ENCFF943DQA, ENCFF976XOX 61728 ENCODE Processing Pipeline 1794332ea2b9cca10525aae42a792c68 https://www.encodeproject.org/files/ENCFF575FVP/@@download/ENCFF575FVP.bed.gz hg19 released control low read depth, low read depth, missing genetic modification characterization ENCFF057EIS bed narrowPeak optimal idr thresholded peaks ENCSR475SOC ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens eGFP-ELF1-human DNA False 2016-06-13 ENCODE 1, 2 ENCFF001TDO, ENCFF270GEP, ENCFF274KQN, ENCFF370CWB 64787 ENCODE Processing Pipeline e08e1fcedfca858311582a55a685cbc9 https://www.encodeproject.org/files/ENCFF057EIS/@@download/ENCFF057EIS.bed.gz hg19 released missing genetic modification characterization ENCFF490VYC bed narrowPeak optimal idr thresholded peaks ENCSR000DZZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TBP-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF052EPC, ENCFF054TZW, ENCFF113YPN 360409 ENCODE Processing Pipeline 83b95b0b1fe7e2d9274f754390afa39e https://www.encodeproject.org/files/ENCFF490VYC/@@download/ENCFF490VYC.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF932CSV bed narrowPeak optimal idr thresholded peaks ENCSR000BMN ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF129OMT, ENCFF623RZZ, ENCFF988BKX 196122 ENCODE Processing Pipeline 6f3de2bcbff211cb74b9c8d2fa8fcbb4 https://www.encodeproject.org/files/ENCFF932CSV/@@download/ENCFF932CSV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth ENCFF312HCK bed narrowPeak optimal idr thresholded peaks ENCSR000DSU ChIP-seq CL:0002606 astrocyte of the spinal cord primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF729AWY, ENCFF892VYV, ENCFF994JFX 765148 ENCODE Processing Pipeline 9dd0d6cf8e5d23c421e1eeffab57d9d4 https://www.encodeproject.org/files/ENCFF312HCK/@@download/ENCFF312HCK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms ENCFF041YQC bed narrowPeak optimal idr thresholded peaks ENCSR000EGW ChIP-seq EFO:0002067 K562 cell line Homo sapiens SMC3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF041YJV, ENCFF714FTS, ENCFF892UIH 454792 ENCODE Processing Pipeline 2933d00ffe16c0f6bdc6e17cf2aa672e https://www.encodeproject.org/files/ENCFF041YQC/@@download/ENCFF041YQC.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF909JAZ bed narrowPeak optimal idr thresholded peaks ENCSR000DKN ChIP-seq EFO:0002782 H54 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF438LOQ, ENCFF618WVP, ENCFF835YPT 843442 ENCODE Processing Pipeline 8fa9219e1759affd4c0fc9fe6cdece07 https://www.encodeproject.org/files/ENCFF909JAZ/@@download/ENCFF909JAZ.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF199WGD bed narrowPeak optimal idr thresholded peaks ENCSR000BGE ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SRF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF339GTZ, ENCFF613VCR, ENCFF972PDN 55949 ENCODE Processing Pipeline edc30706d0e012b4c150f744cbd30f3f https://www.encodeproject.org/files/ENCFF199WGD/@@download/ENCFF199WGD.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF775PPJ bed narrowPeak optimal idr thresholded peaks ENCSR000EDY ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens BRCA1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF698OHI, ENCFF884QMQ, ENCFF890UER 39567 ENCODE Processing Pipeline 275c0cb5c6eb3e6d2abcb295077fbb51 https://www.encodeproject.org/files/ENCFF775PPJ/@@download/ENCFF775PPJ.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF978IWS bed narrowPeak optimal idr thresholded peaks ENCSR000BMO ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXA1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF251GTF, ENCFF596END, ENCFF997MQT 846246 ENCODE Processing Pipeline 7762c6c6fa31a9c99ee27eedaac3b89f https://www.encodeproject.org/files/ENCFF978IWS/@@download/ENCFF978IWS.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth missing control alignments ENCFF721FTG bed narrowPeak optimal idr thresholded peaks ENCSR000EUL ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NR2C2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF258YSG, ENCFF423FMQ, ENCFF973NBX 20872 ENCODE Processing Pipeline abe930e6ea87a09befc3de1e721f6948 https://www.encodeproject.org/files/ENCFF721FTG/@@download/ENCFF721FTG.bed.gz hg19 released borderline replicate concordance, low read depth control insufficient read depth, insufficient read length ENCFF328QLX bed narrowPeak optimal idr thresholded peaks ENCSR000BKB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MEF2A-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF099ZTD, ENCFF951TLZ, ENCFF980AUY 367975 ENCODE Processing Pipeline cff7dbd079130eb4d37ffab592deaa84 https://www.encodeproject.org/files/ENCFF328QLX/@@download/ENCFF328QLX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF002CTM bed narrowPeak optimal idr thresholded peaks ENCSR000EVN ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens NR2C2-human DNA see document see document False 2011-10-29 ENCODE 54026 ENCODE Consortium Analysis Working Group 52ff4a1ff05aae193e3ef1b3b89c71a9 https://www.encodeproject.org/files/ENCFF002CTM/@@download/ENCFF002CTM.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF002CQJ bed narrowPeak optimal idr thresholded peaks ENCSR000EBD ChIP-seq EFO:0005349 GM18951 cell line Homo sapiens tumor necrosis factor 25 ng/mL 6 hour RELA-human DNA see document see document False 2011-10-29 ENCODE 334901 ENCODE Consortium Analysis Working Group 4de97ae097a0b7753657d415a0886a00 https://www.encodeproject.org/files/ENCFF002CQJ/@@download/ENCFF002CQJ.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF940BIM bed narrowPeak optimal idr thresholded peaks ENCSR000BJG ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TCF12-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF080AEE, ENCFF549YBI, ENCFF682QML 82467 ENCODE Processing Pipeline ef10ea189b4f938947aaadfa6b6f4e84 https://www.encodeproject.org/files/ENCFF940BIM/@@download/ENCFF940BIM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient replicate concordance ENCFF372SHI bed narrowPeak optimal idr thresholded peaks ENCSR000DMO ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF569FYX, ENCFF657PRI, ENCFF731UAI 1035407 ENCODE Processing Pipeline 68a0e176e9543319f5c7a612b4098c88 https://www.encodeproject.org/files/ENCFF372SHI/@@download/ENCFF372SHI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample poor library complexity ENCFF593MEB bed narrowPeak optimal idr thresholded peaks ENCSR000EFH ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens MAFK-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF399JDJ, ENCFF497YWO, ENCFF886HLJ 821055 ENCODE Processing Pipeline 038696f5c8018caee2117388898f53fd https://www.encodeproject.org/files/ENCFF593MEB/@@download/ENCFF593MEB.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF446MKT bed narrowPeak optimal idr thresholded peaks ENCSR000DRR ChIP-seq EFO:0001161 GM12874 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF445XBY, ENCFF653LVL, ENCFF961AGO 645559 ENCODE Processing Pipeline 6e25d6e01e8d314d42456184df9c22c7 https://www.encodeproject.org/files/ENCFF446MKT/@@download/ENCFF446MKT.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF606WUV bed narrowPeak optimal idr thresholded peaks ENCSR000BJE ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SIX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF491NVT, ENCFF557TKJ, ENCFF771CBA 91820 ENCODE Processing Pipeline f5cc0ab0fab5aa90cb4d068d46f09c70 https://www.encodeproject.org/files/ENCFF606WUV/@@download/ENCFF606WUV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample severe bottlenecking ENCFF743FCW bed narrowPeak optimal idr thresholded peaks ENCSR000ARE ChIP-seq CL:0002327 mammary epithelial cell primary cell Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF015WVN, ENCFF357WXQ, ENCFF385LJM 144063 ENCODE Processing Pipeline 3dfb5f076fde87b7896b22f33633d866 https://www.encodeproject.org/files/ENCFF743FCW/@@download/ENCFF743FCW.bed.gz hg19 released low read length, borderline replicate concordance, inconsistent platforms ENCFF517YCC bed narrowPeak optimal idr thresholded peaks ENCSR000EFO ChIP-seq EFO:0002067 K562 cell line Homo sapiens CUX1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF599SPU, ENCFF675GZY, ENCFF725FYI 119496 ENCODE Processing Pipeline 2b856671dd29071ba3eec1e8a4e8f69d https://www.encodeproject.org/files/ENCFF517YCC/@@download/ENCFF517YCC.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample missing control alignments ENCFF339KUO bed narrowPeak optimal idr thresholded peaks ENCSR000BHD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens PAX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF252RWC, ENCFF565JQY, ENCFF915CCU 371645 ENCODE Processing Pipeline 6e212171131e6ee7f7d1bc41c78a0c29 https://www.encodeproject.org/files/ENCFF339KUO/@@download/ENCFF339KUO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF913MUA bed narrowPeak optimal idr thresholded peaks ENCSR000BPS ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour ATF3-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF247OWV, ENCFF524QEN, ENCFF556COW 193791 ENCODE Processing Pipeline 88ca13499d91733e358e058e7c845c7c https://www.encodeproject.org/files/ENCFF913MUA/@@download/ENCFF913MUA.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF474KHR bed narrowPeak optimal idr thresholded peaks ENCSR000BOX ChIP-seq EFO:0005234 PFSK-1 cell line Homo sapiens REST-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF655RQF, ENCFF851EOI, ENCFF859NJV 317492 ENCODE Processing Pipeline 54db63fc2e1d8bdcef504e2e0453ac68 https://www.encodeproject.org/files/ENCFF474KHR/@@download/ENCFF474KHR.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample missing control alignments ENCFF002CSW bed narrowPeak optimal idr thresholded peaks ENCSR000EDJ ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens NRF1-human DNA see document see document False 2011-10-29 ENCODE 70752 ENCODE Consortium Analysis Working Group 766b48fd144a543f7d0430424014f1c2 https://www.encodeproject.org/files/ENCFF002CSW/@@download/ENCFF002CSW.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF374ZCG bed narrowPeak optimal idr thresholded peaks ENCSR000BQO ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour FOSL2-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF431AIS, ENCFF912FKQ, ENCFF925WYW 548131 ENCODE Processing Pipeline 7fcebc7d804196dc801fd7220e7c96b9 https://www.encodeproject.org/files/ENCFF374ZCG/@@download/ENCFF374ZCG.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample missing control alignments ENCFF136RBA bed narrowPeak optimal idr thresholded peaks ENCSR000BQP ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour REST-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF621APS, ENCFF719IGT, ENCFF792BHA 334443 ENCODE Processing Pipeline ca1ab14e6137d333433c3bb3c0d8b7bd https://www.encodeproject.org/files/ENCFF136RBA/@@download/ENCFF136RBA.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample ENCFF254MPF bed narrowPeak optimal idr thresholded peaks ENCSR000FAU ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 6.0 hour STAT1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF081YAN, ENCFF873CLE, ENCFF881JMT 23891 ENCODE Processing Pipeline cc0458db40e7d908cb8702d577c43933 https://www.encodeproject.org/files/ENCFF254MPF/@@download/ENCFF254MPF.bed.gz hg19 released control low read depth, borderline replicate concordance biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF248QIW bed narrowPeak optimal idr thresholded peaks ENCSR000BIY ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens estradiol 10 nM 1 hour ESR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF607IFK, ENCFF657XCG, ENCFF895CZK 302156 ENCODE Processing Pipeline a63a02eb5139b8b005ec17f233522dd5 https://www.encodeproject.org/files/ENCFF248QIW/@@download/ENCFF248QIW.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF755AXA bed narrowPeak optimal idr thresholded peaks ENCSR000BRD ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour FOXA1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF420TYJ, ENCFF591IMY, ENCFF605IMH 541926 ENCODE Processing Pipeline 7833f49f8263628cdb770c7d08714a7d https://www.encodeproject.org/files/ENCFF755AXA/@@download/ENCFF755AXA.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF237OKO bed narrowPeak optimal idr thresholded peaks ENCSR000BIE ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CTCF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF297IFU, ENCFF327TVJ, ENCFF487OYC 948053 ENCODE Processing Pipeline 13e337503a6a9deb5c4953281268d9fa https://www.encodeproject.org/files/ENCFF237OKO/@@download/ENCFF237OKO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample missing control alignments ENCFF525EJQ bed narrowPeak optimal idr thresholded peaks ENCSR000EDW ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens SMC3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF382SIS, ENCFF620MYW, ENCFF672PNA 593833 ENCODE Processing Pipeline 1b4f67a75954ebc5d1390e20bb29420b https://www.encodeproject.org/files/ENCFF525EJQ/@@download/ENCFF525EJQ.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF853SOB bed narrowPeak optimal idr thresholded peaks ENCSR000DZJ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BHLHE40-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF354WUJ, ENCFF512QTF, ENCFF909EYB 407249 ENCODE Processing Pipeline d964abe4d5ff7ce20874db90631d395f https://www.encodeproject.org/files/ENCFF853SOB/@@download/ENCFF853SOB.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF019PEL bed narrowPeak optimal idr thresholded peaks ENCSR000EFU ChIP-seq EFO:0002067 K562 cell line Homo sapiens ELK1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF324CAS, ENCFF390VNW, ENCFF670YGF 72723 ENCODE Processing Pipeline 6bef1c87b6be232eb240e302cc14670d https://www.encodeproject.org/files/ENCFF019PEL/@@download/ENCFF019PEL.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF150VTD bed narrowPeak optimal idr thresholded peaks ENCSR000EHG ChIP-seq EFO:0002067 K562 cell line Homo sapiens USF2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF129CHM, ENCFF505EIB, ENCFF935ZZG 66396 ENCODE Processing Pipeline 374d6db908c4b58361da86e304486f3d https://www.encodeproject.org/files/ENCFF150VTD/@@download/ENCFF150VTD.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002DCY bed narrowPeak optimal idr thresholded peaks ENCSR000DUH ChIP-seq CL:1001608 foreskin fibroblast primary cell Homo sapiens CTCF-human DNA see document see document False 2012-02-29 ENCODE 1 ENCFF001HNZ 680211 ENCODE Consortium Analysis Working Group e3c022ea9f7be7acf4d1ea7ccf3b03e6 https://www.encodeproject.org/files/ENCFF002DCY/@@download/ENCFF002DCY.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF800XTT bed narrowPeak optimal idr thresholded peaks ENCSR000EDZ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MAFK-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF227YDJ, ENCFF422YLS, ENCFF700LQD 806864 ENCODE Processing Pipeline 438973c4146937122e69e33c208d92a0 https://www.encodeproject.org/files/ENCFF800XTT/@@download/ENCFF800XTT.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF048JKT bed narrowPeak optimal idr thresholded peaks ENCSR000BGF ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF022KXM, ENCFF562ZXJ, ENCFF632AEM 104093 ENCODE Processing Pipeline 821185bde94cd93d206c629d07774040 https://www.encodeproject.org/files/ENCFF048JKT/@@download/ENCFF048JKT.bed.gz hg19 released low read length, low read depth, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF753RGL bed narrowPeak optimal idr thresholded peaks ENCSR000BMY ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RAD21-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF436OWU, ENCFF510UIU, ENCFF601GLM 688110 ENCODE Processing Pipeline c297cd9f39ea9fa917cc79632b77b70d https://www.encodeproject.org/files/ENCFF753RGL/@@download/ENCFF753RGL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF584CNF bed narrowPeak optimal idr thresholded peaks ENCSR000EEL ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TBP-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF469IRK, ENCFF791JVM, ENCFF967KDT 324761 ENCODE Processing Pipeline f69505c8d4f6d551de135c08ff65c0d3 https://www.encodeproject.org/files/ENCFF584CNF/@@download/ENCFF584CNF.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF012VES bed narrowPeak optimal idr thresholded peaks ENCSR000EGR ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFYA-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF003WYE, ENCFF690KLI, ENCFF711NWL 77635 ENCODE Processing Pipeline ead81452d9d50afa34b4539574d408f5 https://www.encodeproject.org/files/ENCFF012VES/@@download/ENCFF012VES.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity biological replicates with identical biosample insufficient read depth, insufficient read length extremely low read depth ENCFF344QKL bed narrowPeak optimal idr thresholded peaks ENCSR000EVX ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF274-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF479ZWB, ENCFF854CCF, ENCFF904PBE 56693 ENCODE Processing Pipeline e1dcb354f98030f0cad5ea10cb6b8428 https://www.encodeproject.org/files/ENCFF344QKL/@@download/ENCFF344QKL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample ENCFF114IWY bed narrowPeak optimal idr thresholded peaks ENCSR000EGP ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF143-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF178ANU, ENCFF971SGR, ENCFF984KWO 507074 ENCODE Processing Pipeline 2080efa4f0591f3162e78e92da027eb5 https://www.encodeproject.org/files/ENCFF114IWY/@@download/ENCFF114IWY.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF195PBG bed narrowPeak optimal idr thresholded peaks ENCSR000DYQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ESRRA-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF430QIK, ENCFF894NTO, ENCFF927WFK 93614 ENCODE Processing Pipeline 3efe3e9ba0dd7bc225ff4fec1d74a0a8 https://www.encodeproject.org/files/ENCFF195PBG/@@download/ENCFF195PBG.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF111IPG bed narrowPeak optimal idr thresholded peaks ENCSR000DOP ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens afimoxifene 1.0 μM 12.0 hour FOS-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF177VFU, ENCFF245IKC, ENCFF364ZNH 1625733 ENCODE Processing Pipeline 46234c121cddbc9360b1cf51d8a0bc48 https://www.encodeproject.org/files/ENCFF111IPG/@@download/ENCFF111IPG.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity, missing genetic modification characterization biological replicates with identical biosample, duplicate lane review ENCFF244DQW bed narrowPeak optimal idr thresholded peaks ENCSR000DLG ChIP-seq EFO:0005352 GM20000 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF128FLJ, ENCFF192ODH, ENCFF780CML 438676 ENCODE Processing Pipeline 0c21dfd74bd1ff0c763735b180ac1d59 https://www.encodeproject.org/files/ENCFF244DQW/@@download/ENCFF244DQW.bed.gz hg19 released control low read depth, mild to moderate bottlenecking biological replicates with identical biosample insufficient read depth missing control alignments ENCFF002DBL bed narrowPeak optimal idr thresholded peaks ENCSR000DML ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1161292 ENCODE Consortium Analysis Working Group ea48635d4b9f9f1045e967c2f5e54d78 https://www.encodeproject.org/files/ENCFF002DBL/@@download/ENCFF002DBL.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample, missing derived_from ENCFF474NLG bed narrowPeak optimal idr thresholded peaks ENCSR000EFN ChIP-seq EFO:0002067 K562 cell line Homo sapiens HCFC1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF317AIN, ENCFF386FIZ, ENCFF912AHN 236039 ENCODE Processing Pipeline fe108db88c03657b64f8b0ec52bd7c3e https://www.encodeproject.org/files/ENCFF474NLG/@@download/ENCFF474NLG.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF328XKC bed narrowPeak optimal idr thresholded peaks ENCSR000BMH ChIP-seq EFO:0002067 K562 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF223XFI, ENCFF701OSU, ENCFF720DVS 497639 ENCODE Processing Pipeline 01d30b98e8410f018839a27847bfd7fc https://www.encodeproject.org/files/ENCFF328XKC/@@download/ENCFF328XKC.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF933GHY bed narrowPeak optimal idr thresholded peaks ENCSR000EEA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RFX5-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF003GUP, ENCFF304RUP, ENCFF777PZJ 138519 ENCODE Processing Pipeline 27647aa248b0cf30ae4671167b3b5fa0 https://www.encodeproject.org/files/ENCFF933GHY/@@download/ENCFF933GHY.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample missing control alignments ENCFF021KDL bed narrowPeak optimal idr thresholded peaks ENCSR000DMJ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MYC-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF341DDR, ENCFF373LWH, ENCFF808TOF 179969 ENCODE Processing Pipeline 806e8f646a0ceaa45c7766f5667a367e https://www.encodeproject.org/files/ENCFF021KDL/@@download/ENCFF021KDL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF499QUE bed narrowPeak optimal idr thresholded peaks ENCSR000BLL ChIP-seq EFO:0001247 T47D cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour ESR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF372ATJ, ENCFF593GDN, ENCFF664LLB 67651 ENCODE Processing Pipeline f67dc576679a3b4f475e5598c9bf2068 https://www.encodeproject.org/files/ENCFF499QUE/@@download/ENCFF499QUE.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample insufficient replicate concordance ENCFF706SJZ bed narrowPeak optimal idr thresholded peaks ENCSR000EFP ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF384-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF319WWO, ENCFF722BEI, ENCFF913KLO 354973 ENCODE Processing Pipeline 8b78ea00785bf7a9dc6f64503042fe49 https://www.encodeproject.org/files/ENCFF706SJZ/@@download/ENCFF706SJZ.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF841RSF bed narrowPeak optimal idr thresholded peaks ENCSR000EXH ChIP-seq EFO:0005236 NT2/D1 cell line Homo sapiens SUZ12-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF203YKR, ENCFF258BUQ, ENCFF259PLY 114990 ENCODE Processing Pipeline f775fe62ab6cbe2bfc618f009a319d9b https://www.encodeproject.org/files/ENCFF841RSF/@@download/ENCFF841RSF.bed.gz hg19 released biological replicates with identical biosample insufficient read depth, insufficient read length extremely low read depth ENCFF414JLN bed narrowPeak optimal idr thresholded peaks ENCSR000DNN ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFYA-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF063ESL, ENCFF333CPM, ENCFF423EOR 21975 ENCODE Processing Pipeline 151656e4361aa7092b6b3591b2f30ddb https://www.encodeproject.org/files/ENCFF414JLN/@@download/ENCFF414JLN.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF867ERM bed narrowPeak optimal idr thresholded peaks ENCSR000DND ChIP-seq UBERON:0001264 pancreas tissue Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF329BNL, ENCFF417BGF, ENCFF427RBA 506571 ENCODE Processing Pipeline 5db1c38f26beabf07a70b2a3a8e67817 https://www.encodeproject.org/files/ENCFF867ERM/@@download/ENCFF867ERM.bed.gz hg19 released control low read depth, mild to moderate bottlenecking extremely low read depth, missing control alignments ENCFF570FLB bed narrowPeak optimal idr thresholded peaks ENCSR000DVA ChIP-seq CL:0002553 fibroblast of lung primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF129FBO, ENCFF213JJM, ENCFF519REF 763178 ENCODE Processing Pipeline 86c192815799a1a048cd599e0a046fe5 https://www.encodeproject.org/files/ENCFF570FLB/@@download/ENCFF570FLB.bed.gz hg19 released control low read depth, low read length, low read depth, inconsistent platforms ENCFF857YVK bed narrowPeak optimal idr thresholded peaks ENCSR000BKE ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ATF3-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF291WLP, ENCFF414JVR, ENCFF725ZKM 73270 ENCODE Processing Pipeline 9b4d7d6214441c243d20fe05b2418338 https://www.encodeproject.org/files/ENCFF857YVK/@@download/ENCFF857YVK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF002CUV bed narrowPeak optimal idr thresholded peaks ENCSR000EEO ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens insulin and 22-hydroxycholesterol 6.0 hour SREBF1-human DNA see document see document False 2011-10-29 ENCODE 69298 ENCODE Consortium Analysis Working Group 1ce43dcd4aef03944a74077ca1acebe5 https://www.encodeproject.org/files/ENCFF002CUV/@@download/ENCFF002CUV.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF379EPK bed narrowPeak optimal idr thresholded peaks ENCSR000BMT ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens NANOG-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF482QCD, ENCFF537QBW, ENCFF637UCH 146369 ENCODE Processing Pipeline 7ca39501c1ae70ddd76818ac016a1ea6 https://www.encodeproject.org/files/ENCFF379EPK/@@download/ENCFF379EPK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms biological replicates with identical biosample insufficient read depth, poor library complexity, severe bottlenecking ENCFF418RZE bed narrowPeak optimal idr thresholded peaks ENCSR000BNS ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens FOSL1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF338LQY, ENCFF754FCZ, ENCFF823FFU 22674 ENCODE Processing Pipeline 545aadabf867370d3f560aacd02b24a1 https://www.encodeproject.org/files/ENCFF418RZE/@@download/ENCFF418RZE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF881YDR bed narrowPeak optimal idr thresholded peaks ENCSR000DNI ChIP-seq UBERON:0002106 spleen tissue Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF250AFB, ENCFF307XCC, ENCFF310RCE 616195 ENCODE Processing Pipeline 57dc061a40055e9cafafda1448190a37 https://www.encodeproject.org/files/ENCFF881YDR/@@download/ENCFF881YDR.bed.gz hg19 released mild to moderate bottlenecking, low read depth, moderate library complexity control insufficient read depth, insufficient read depth missing control alignments ENCFF310XJC bed narrowPeak optimal idr thresholded peaks ENCSR000DNQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZZZ3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF063ECO, ENCFF833VKG, ENCFF908NXJ 11888 ENCODE Processing Pipeline c74d3fcbe69e36a64d3a973909d60c6a https://www.encodeproject.org/files/ENCFF310XJC/@@download/ENCFF310XJC.bed.gz hg19 released low read depth biological replicates with identical biosample control insufficient read depth, insufficient read length ENCFF609KOY bed narrowPeak optimal idr thresholded peaks ENCSR000BQK ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ATF2-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF071BNB, ENCFF378GKG, ENCFF599NQC 516541 ENCODE Processing Pipeline 64817c03f12a08a77eb97b9c2fabe83d https://www.encodeproject.org/files/ENCFF609KOY/@@download/ENCFF609KOY.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample ENCFF002DBD bed narrowPeak optimal idr thresholded peaks ENCSR000DMA ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1077102 ENCODE Consortium Analysis Working Group 691e48b1344e23067ee35e35c640d364 https://www.encodeproject.org/files/ENCFF002DBD/@@download/ENCFF002DBD.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read depth, insufficient read length extremely low read depth ENCFF002CVS bed narrowPeak optimal idr thresholded peaks ENCSR000DOC ChIP-seq EFO:0002067 K562 cell line Homo sapiens BRF2-human DNA see document see document False 2011-10-29 ENCODE 29151 ENCODE Consortium Analysis Working Group f075234fcb2722a9724e3854f969ff0b https://www.encodeproject.org/files/ENCFF002CVS/@@download/ENCFF002CVS.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF255XVM bed narrowPeak optimal idr thresholded peaks ENCSR000DPB ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens afimoxifene 1.0 μM 36.0 hour STAT3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF496UPK, ENCFF691LNH, ENCFF819FYL 850994 ENCODE Processing Pipeline 07b01799230f5ce63cae89d51b676ccb https://www.encodeproject.org/files/ENCFF255XVM/@@download/ENCFF255XVM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF514OYL bed narrowPeak optimal idr thresholded peaks ENCSR000EDP ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ARID3A-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF287ZJM, ENCFF542DWV, ENCFF723URK 413265 ENCODE Processing Pipeline 1b3c1634fb8c0f173c3d5f60070ce2e3 https://www.encodeproject.org/files/ENCFF514OYL/@@download/ENCFF514OYL.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF300IYQ bed narrowPeak optimal idr thresholded peaks ENCSR000DNA ChIP-seq EFO:0001086 A549 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF290ZCZ, ENCFF537TSK, ENCFF865ANK 693513 ENCODE Processing Pipeline 654e0d3526208ce14b7a33232e365a5a https://www.encodeproject.org/files/ENCFF300IYQ/@@download/ENCFF300IYQ.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF402ELS bed narrowPeak optimal idr thresholded peaks ENCSR000ECA ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens JUN-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF115XCV, ENCFF622NKF, ENCFF961BTT 48603 ENCODE Processing Pipeline 1840846ef482a55692abf6313aec1279 https://www.encodeproject.org/files/ENCFF402ELS/@@download/ENCFF402ELS.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF749OBU bed narrowPeak optimal idr thresholded peaks ENCSR000ECD ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens USF2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF019JVF, ENCFF264NVN, ENCFF846OWC 152905 ENCODE Processing Pipeline 4b435ca82f521bf3df4bfd0f305c0d06 https://www.encodeproject.org/files/ENCFF749OBU/@@download/ENCFF749OBU.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF002DDO bed narrowPeak optimal idr thresholded peaks ENCSR000DWY ChIP-seq CL:0002553 fibroblast of lung primary cell Homo sapiens CTCF-human DNA see document see document False 2012-02-29 ENCODE 1 ENCFF001HVT 711922 ENCODE Consortium Analysis Working Group bc64fef4c49c1c68c531c03381fb685f https://www.encodeproject.org/files/ENCFF002DDO/@@download/ENCFF002DDO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF202SNU bed narrowPeak optimal idr thresholded peaks ENCSR000BHO ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF084XPA, ENCFF361YHU, ENCFF967ZPP 484992 ENCODE Processing Pipeline 80c3d936154d88a4a35c94bd1f3b8842 https://www.encodeproject.org/files/ENCFF202SNU/@@download/ENCFF202SNU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF083KVY bed narrowPeak optimal idr thresholded peaks ENCSR000DZF ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MAX-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF173DKW, ENCFF694JRS, ENCFF974XPG 337281 ENCODE Processing Pipeline 951409976105220a24dc6e8cf17d2090 https://www.encodeproject.org/files/ENCFF083KVY/@@download/ENCFF083KVY.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF746CIL bed narrowPeak optimal idr thresholded peaks ENCSR000DPV ChIP-seq NTR:0000481 AG10803 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF025STW, ENCFF229WQW, ENCFF934ZVZ 805043 ENCODE Processing Pipeline a854e71bdfcc17eb98e8c2ff896d8bbb https://www.encodeproject.org/files/ENCFF746CIL/@@download/ENCFF746CIL.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms NTR biosample ENCFF972NIR bed narrowPeak optimal idr thresholded peaks ENCSR000EEH ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NRF1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF228KKV, ENCFF864QJF, ENCFF966VOH 38996 ENCODE Processing Pipeline 9279471da999b426ccbb6fc9df0cb304 https://www.encodeproject.org/files/ENCFF972NIR/@@download/ENCFF972NIR.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF073XZC bed narrowPeak optimal idr thresholded peaks ENCSR000EUJ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens IKZF1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF330XDW, ENCFF723VGS, ENCFF742JAC 239645 ENCODE Processing Pipeline 1e25bdbd10c76538c1fc79f86e4ff09f https://www.encodeproject.org/files/ENCFF073XZC/@@download/ENCFF073XZC.bed.gz hg19 released low read length, low read depth control insufficient read depth ENCFF836LBG bed narrowPeak optimal idr thresholded peaks ENCSR000EWE ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF274-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF337RTD, ENCFF556HBG, ENCFF565OZP 7351 ENCODE Processing Pipeline ee40819a3e319921e26d72427860725d https://www.encodeproject.org/files/ENCFF836LBG/@@download/ENCFF836LBG.bed.gz hg19 released biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF319HLW bed narrowPeak optimal idr thresholded peaks ENCSR618ICR ChIP-seq EFO:0001086 A549 cell line Homo sapiens RCOR1-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF105LXO, ENCFF348XCJ, ENCFF821INE 14457 ENCODE Processing Pipeline 13a3b524ef8f07cfa68348b0e7880fa3 https://www.encodeproject.org/files/ENCFF319HLW/@@download/ENCFF319HLW.bed.gz hg19 released file validation error, low read length, low read depth, antibody characterized with exemption mismatched file status ENCFF874PNQ bed narrowPeak optimal idr thresholded peaks ENCSR000BLY ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens all-trans-retinoic acid 6 μM 48 hour RAD21-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF114SKT, ENCFF758GUY, ENCFF846NCI 1108510 ENCODE Processing Pipeline 6578f7d35c36ea6f9b39a78cd0131e2d https://www.encodeproject.org/files/ENCFF874PNQ/@@download/ENCFF874PNQ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF002CSO bed narrowPeak optimal idr thresholded peaks ENCSR000EDF ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens IRF3-human DNA see document see document False 2011-10-29 ENCODE 42861 ENCODE Consortium Analysis Working Group 61be13789db82a32b707fa71aa317854 https://www.encodeproject.org/files/ENCFF002CSO/@@download/ENCFF002CSO.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF686FLD bed narrowPeak optimal idr thresholded peaks ENCSR000DZP ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SMC3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF027ZKP, ENCFF246ZRW, ENCFF249QCH 573680 ENCODE Processing Pipeline bba9c26b2d0c073aaa60505f9cfdb10b https://www.encodeproject.org/files/ENCFF686FLD/@@download/ENCFF686FLD.bed.gz hg19 released low read length, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF894MNP bed narrowPeak optimal idr thresholded peaks ENCSR000BIW ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens GABPA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF027RYJ, ENCFF352YTI, ENCFF814FEG 169751 ENCODE Processing Pipeline 35b95ff5dd3e74989c0a226c380141bd https://www.encodeproject.org/files/ENCFF894MNP/@@download/ENCFF894MNP.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF002CSR bed narrowPeak optimal idr thresholded peaks ENCSR000ECN ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MAX-human DNA see document see document False 2012-05-14 ENCODE 742112 ENCODE Consortium Analysis Working Group 4e2babbda793ba249e6f4ed5048b3462 https://www.encodeproject.org/files/ENCFF002CSR/@@download/ENCFF002CSR.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF588NYF bed narrowPeak optimal idr thresholded peaks ENCSR000BMF ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens all-trans-retinoic acid 6 μM 48 hour USF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF110YHD, ENCFF481EBP, ENCFF872MXG 359763 ENCODE Processing Pipeline dd7204e1356625205a7ae66985c33cd6 https://www.encodeproject.org/files/ENCFF588NYF/@@download/ENCFF588NYF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF958LUB bed narrowPeak optimal idr thresholded peaks ENCSR000BLZ ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens all-trans-retinoic acid 6 μM 48 hour YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF008AIJ, ENCFF310NCC, ENCFF477NKZ 402582 ENCODE Processing Pipeline 3865699116468e4950ef588d5cb2ba3e https://www.encodeproject.org/files/ENCFF958LUB/@@download/ENCFF958LUB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF305QDB bed narrowPeak optimal idr thresholded peaks ENCSR000BHT ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF533OIU, ENCFF558HCQ, ENCFF570CST 312444 ENCODE Processing Pipeline 212dacefd25c5361bc1b2e5400f36d9c https://www.encodeproject.org/files/ENCFF305QDB/@@download/ENCFF305QDB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth ENCFF429XKT bed narrowPeak optimal idr thresholded peaks ENCSR000EHE ChIP-seq EFO:0002067 K562 cell line Homo sapiens CEBPB-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF143EHM, ENCFF206BMO, ENCFF755NTM 766395 ENCODE Processing Pipeline 88c12b16ffd687378e1854b5f80644c8 https://www.encodeproject.org/files/ENCFF429XKT/@@download/ENCFF429XKT.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF156WRH bed narrowPeak optimal idr thresholded peaks ENCSR000EHC ChIP-seq EFO:0002067 K562 cell line Homo sapiens GTF2F1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF123HUT, ENCFF220GLK, ENCFF614RPL 94699 ENCODE Processing Pipeline 3412d376260c85c185a7efc28f868928 https://www.encodeproject.org/files/ENCFF156WRH/@@download/ENCFF156WRH.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF573GQX bed narrowPeak optimal idr thresholded peaks ENCSR000EZX ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 6.0 hour JUN-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF041POZ, ENCFF605EZB, ENCFF829NXG 84349 ENCODE Processing Pipeline abed910a74ad73f3c1db21033f7275f3 https://www.encodeproject.org/files/ENCFF573GQX/@@download/ENCFF573GQX.bed.gz hg19 released control low read depth biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF337DKJ bed narrowPeak optimal idr thresholded peaks ENCSR000EGN ChIP-seq EFO:0002067 K562 cell line Homo sapiens JUND-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF159IRT, ENCFF367HPL, ENCFF844LUC 761693 ENCODE Processing Pipeline 3a2d773ef2c1c39f7ac48b0924f2febe https://www.encodeproject.org/files/ENCFF337DKJ/@@download/ENCFF337DKJ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CVP bed narrowPeak optimal idr thresholded peaks ENCSR000DOK ChIP-seq EFO:0002067 K562 cell line Homo sapiens BDP1-human DNA see document see document False 2011-10-29 ENCODE 14731 ENCODE Consortium Analysis Working Group b7736965c422593b231caef94ba62e82 https://www.encodeproject.org/files/ENCFF002CVP/@@download/ENCFF002CVP.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF116EXQ bed narrowPeak optimal idr thresholded peaks ENCSR331HPA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens GABPA-human DNA False 2014-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF304VXR, ENCFF379IZI, ENCFF636JXY 145088 ENCODE Processing Pipeline 54561d7676f209c4accf47a9d8d8dbda https://www.encodeproject.org/files/ENCFF116EXQ/@@download/ENCFF116EXQ.bed.gz hg19 released mild to moderate bottlenecking, low read depth, inconsistent platforms, antibody characterized with exemption biological replicates with identical biosample ENCFF030NYG bed narrowPeak optimal idr thresholded peaks ENCSR000BMI ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SRF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF252ZSU, ENCFF256FUR, ENCFF694IUT 198820 ENCODE Processing Pipeline bc1bb5c6d32dc9c8b9ce28c46e4b77e4 https://www.encodeproject.org/files/ENCFF030NYG/@@download/ENCFF030NYG.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF220IXP bed narrowPeak optimal idr thresholded peaks ENCSR000BJA ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens EGR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF235LAV, ENCFF283VJO, ENCFF375CPS 205136 ENCODE Processing Pipeline 3264aafab10c53352fc8b19ad9cc0ac5 https://www.encodeproject.org/files/ENCFF220IXP/@@download/ENCFF220IXP.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample ENCFF617AHB bed narrowPeak optimal idr thresholded peaks ENCSR945NFL ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens USF2-human DNA False 2017-06-15 ENCODE 1, 2 ENCFF001TDO, ENCFF168LBA, ENCFF680TFE, ENCFF982EXB 17167 ENCODE Processing Pipeline 2c2a17a597bd629f495146a50ff1ed9b https://www.encodeproject.org/files/ENCFF617AHB/@@download/ENCFF617AHB.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, antibody characterized with exemption ENCFF077UYM bed narrowPeak optimal idr thresholded peaks ENCSR000EGH ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 30.0 minute JUN-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF063HEH, ENCFF257FNC, ENCFF767GKW 166535 ENCODE Processing Pipeline 1bfdc3d3c368a4f534014f7554f50dcd https://www.encodeproject.org/files/ENCFF077UYM/@@download/ENCFF077UYM.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF855HSK bed narrowPeak optimal idr thresholded peaks ENCSR000DKR ChIP-seq EFO:0005335 GM10266 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF327KKL, ENCFF787CXT, ENCFF950YTB 520860 ENCODE Processing Pipeline 88e4bb9295bf0a07c811034ba0e4ed00 https://www.encodeproject.org/files/ENCFF855HSK/@@download/ENCFF855HSK.bed.gz hg19 released mild to moderate bottlenecking, low read depth biological replicates with identical biosample control insufficient read depth missing control alignments ENCFF002CSJ bed narrowPeak optimal idr thresholded peaks ENCSR000ECI ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ELK1-human DNA see document see document False 2012-05-14 ENCODE 128199 ENCODE Consortium Analysis Working Group 68b83db449782d8ce122a93a2d7a85b9 https://www.encodeproject.org/files/ENCFF002CSJ/@@download/ENCFF002CSJ.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from, duplicate lane review ENCFF772PCI bed narrowPeak optimal idr thresholded peaks ENCSR000DOS ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens ethanol 0.01 percent 36.0 hour MYC-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF190UWS, ENCFF485KEP, ENCFF660LCY 667279 ENCODE Processing Pipeline 480e952f21e9a364c2c650596739204d https://www.encodeproject.org/files/ENCFF772PCI/@@download/ENCFF772PCI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, missing genetic modification characterization biological replicates with identical biosample ENCFF629MBV bed narrowPeak optimal idr thresholded peaks ENCSR000ECB ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens TBP-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF208DFV, ENCFF686GYI, ENCFF730GTB 395270 ENCODE Processing Pipeline 1461e05d9f74c404801d4b756e9f4c7e https://www.encodeproject.org/files/ENCFF629MBV/@@download/ENCFF629MBV.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF835KAT bed narrowPeak optimal idr thresholded peaks ENCSR000EFY ChIP-seq EFO:0002067 K562 cell line Homo sapiens ARID3A-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF378JGJ, ENCFF411VNI, ENCFF732QKX 203969 ENCODE Processing Pipeline 61a07b9ac21ac0103491a01c337814c1 https://www.encodeproject.org/files/ENCFF835KAT/@@download/ENCFF835KAT.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF924OMX bed narrowPeak optimal idr thresholded peaks ENCSR000DXW ChIP-seq EFO:0005715 WERI-Rb-1 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF437VBU, ENCFF641GOK, ENCFF837XNW 890963 ENCODE Processing Pipeline 85e198d151d13048fd43f592ae2d1063 https://www.encodeproject.org/files/ENCFF924OMX/@@download/ENCFF924OMX.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms insufficient read depth ENCFF274AQE bed narrowPeak optimal idr thresholded peaks ENCSR000BIT ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens TCF12-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF143RTQ, ENCFF447CBR, ENCFF500IOB 194337 ENCODE Processing Pipeline faca2edfad31759b309588367cc6d3bb https://www.encodeproject.org/files/ENCFF274AQE/@@download/ENCFF274AQE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth missing control alignments ENCFF862VFJ bed narrowPeak optimal idr thresholded peaks ENCSR027HML ChIP-seq EFO:0006711 OCI-LY7 cell line Homo sapiens CTCF-human DNA see document see document False 2014-07-11 ENCODE 1, 2 ENCFF001TDO, ENCFF344EMX, ENCFF536OEM, ENCFF607FHS 1500244 ENCODE Processing Pipeline 3ea35f80ad188673c48542f634d09d79 https://www.encodeproject.org/files/ENCFF862VFJ/@@download/ENCFF862VFJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity, mixed read lengths, antibody characterized with exemption NTR biosample ENCFF002CSB bed narrowPeak optimal idr thresholded peaks ENCSR000EZE ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens FOS-human DNA see document see document False 2011-10-29 ENCODE 233892 ENCODE Consortium Analysis Working Group d1cdae9ffcf36c5c0bd31a65c7f33126 https://www.encodeproject.org/files/ENCFF002CSB/@@download/ENCFF002CSB.bed.gz hg19 released inconsistent platforms duplicate lane review, missing derived_from, biological replicates with identical biosample insufficient read length ENCFF658OOS bed narrowPeak optimal idr thresholded peaks ENCSR000EBX ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens BRCA1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF312BLK, ENCFF354QYP, ENCFF607PGS 36525 ENCODE Processing Pipeline 84b058d22a0501bc42a348af3a655419 https://www.encodeproject.org/files/ENCFF658OOS/@@download/ENCFF658OOS.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF544XKC bed narrowPeak optimal idr thresholded peaks ENCSR115SMW ChIP-seq EFO:0002067 K562 cell line Homo sapiens PKNOX1-human DNA False 2016-06-14 ENCODE 1, 2 ENCFF001TDO, ENCFF279KYF, ENCFF572VXK, ENCFF967UHQ 884225 ENCODE Processing Pipeline 1be1447808c5db1b66e6c0b3f3cf0782 https://www.encodeproject.org/files/ENCFF544XKC/@@download/ENCFF544XKC.bed.gz hg19 released ENCFF649IRT bed narrowPeak optimal idr thresholded peaks ENCSR000DQI ChIP-seq EFO:0002779 BJ cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF493VQC, ENCFF777VSN, ENCFF829XOU 747549 ENCODE Processing Pipeline cff73f0abc942e1a9b0fc2c314cef00e https://www.encodeproject.org/files/ENCFF649IRT/@@download/ENCFF649IRT.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth insufficient read depth ENCFF563QBC bed narrowPeak optimal idr thresholded peaks ENCSR000BJZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BCLAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF590VTP, ENCFF591DYQ, ENCFF596IAY 384864 ENCODE Processing Pipeline dbc8a781e1fbe9d3923a0952f41aab3f https://www.encodeproject.org/files/ENCFF563QBC/@@download/ENCFF563QBC.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF586TYX bed narrowPeak optimal idr thresholded peaks ENCSR261VAS ChIP-seq CL:0000192 smooth muscle cell in vitro differentiated cells Homo sapiens CTCF-human DNA False 2017-12-03 ENCODE 1, 2 ENCFF001TDO, ENCFF339XVK, ENCFF343NOG, ENCFF456RUF 675274 ENCODE Processing Pipeline 2ac43f62ae79b7d5f01a73fcd51ae244 https://www.encodeproject.org/files/ENCFF586TYX/@@download/ENCFF586TYX.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, antibody characterized with exemption NTR biosample, experiment not submitted to GEO insufficient read depth, poor library complexity, severe bottlenecking ENCFF423EMU bed narrowPeak optimal idr thresholded peaks ENCSR000EGD ChIP-seq EFO:0002067 K562 cell line Homo sapiens BACH1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF091TOR, ENCFF107CCL, ENCFF276CQA 88613 ENCODE Processing Pipeline 4a5e60199fc2e91ed05449790c0ead65 https://www.encodeproject.org/files/ENCFF423EMU/@@download/ENCFF423EMU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF859PRV bed narrowPeak optimal idr thresholded peaks ENCSR000DPY ChIP-seq CL:0002547 fibroblast of the aortic adventitia primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF005RNW, ENCFF241LIY, ENCFF567GAL 779989 ENCODE Processing Pipeline 43616394b9f92fa49f35482cff6b7155 https://www.encodeproject.org/files/ENCFF859PRV/@@download/ENCFF859PRV.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms insufficient read depth ENCFF305HBV bed narrowPeak optimal idr thresholded peaks ENCSR000BKC ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens ATF3-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF067KOU, ENCFF450PVT, ENCFF616DKI 92829 ENCODE Processing Pipeline 742a86a42182a571b8d1fb3cf02d9b7b https://www.encodeproject.org/files/ENCFF305HBV/@@download/ENCFF305HBV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth ENCFF851XSC bed narrowPeak optimal idr thresholded peaks ENCSR000EFF ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens MAZ-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF574TBH, ENCFF958APN, ENCFF978ATS 509179 ENCODE Processing Pipeline c30f2d65f9f1570a7e3ee65baba3006e https://www.encodeproject.org/files/ENCFF851XSC/@@download/ENCFF851XSC.bed.gz hg19 released borderline replicate concordance, moderate library complexity, inconsistent target of control experiment, low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF014RBU bed narrowPeak optimal idr thresholded peaks ENCSR000DZV ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens STAT3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF211SUY, ENCFF234PNC, ENCFF318RHH 135992 ENCODE Processing Pipeline 22bf3b30438a5ab0a401f82cf845218f https://www.encodeproject.org/files/ENCFF014RBU/@@download/ENCFF014RBU.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CVN bed narrowPeak optimal idr thresholded peaks ENCSR000DOG ChIP-seq EFO:0002067 K562 cell line Homo sapiens ATF3-human DNA see document see document False 2011-10-29 ENCODE 30756 ENCODE Consortium Analysis Working Group f96359d316397bebb076f46153d104bf https://www.encodeproject.org/files/ENCFF002CVN/@@download/ENCFF002CVN.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF733YSO bed narrowPeak optimal idr thresholded peaks ENCSR000DRU ChIP-seq EFO:0001162 GM12875 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF046FAZ, ENCFF737TLI, ENCFF852LHB 648391 ENCODE Processing Pipeline d2404a9f8ac0a0b865ac97ec3f6460e4 https://www.encodeproject.org/files/ENCFF733YSO/@@download/ENCFF733YSO.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth ENCFF677KJB bed narrowPeak optimal idr thresholded peaks ENCSR000BQS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens REST-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF294FPR, ENCFF793WOV, ENCFF974PTU 109221 ENCODE Processing Pipeline 0c909169189fe56ee39c28dcf7ff48fa https://www.encodeproject.org/files/ENCFF677KJB/@@download/ENCFF677KJB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth ENCFF002DDJ bed narrowPeak optimal idr thresholded peaks ENCSR000DWE ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001HTC, ENCFF001HTD 869756 ENCODE Consortium Analysis Working Group 8e9f23cdfc27292f8fc0f0b302cd296a https://www.encodeproject.org/files/ENCFF002DDJ/@@download/ENCFF002DDJ.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms insufficient read depth, poor library complexity, severe bottlenecking ENCFF556JBS bed narrowPeak optimal idr thresholded peaks ENCSR000DZB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ELK1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF304FFB, ENCFF457WBU, ENCFF839VSW 137008 ENCODE Processing Pipeline 8a3f9f934ad6fb0dc377fb2d047121b3 https://www.encodeproject.org/files/ENCFF556JBS/@@download/ENCFF556JBS.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF002ROJ bed narrowPeak optimal idr thresholded peaks ENCSR000BNI ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXA2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF767MET, ENCFF782XTI, ENCFF850ZXW 823038 ENCODE Processing Pipeline 5e3ca1038ebee9259751b5b2bc902c3a https://www.encodeproject.org/files/ENCFF002ROJ/@@download/ENCFF002ROJ.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample insufficient read depth, poor library complexity, insufficient replicate concordance, severe bottlenecking ENCFF002COM bed narrowPeak optimal idr thresholded peaks ENCSR000EYZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens FOS-human DNA see document see document False 2011-10-29 ENCODE 55234 ENCODE Consortium Analysis Working Group f1d429a4e067d67537009d22f43162c8 https://www.encodeproject.org/files/ENCFF002COM/@@download/ENCFF002COM.bed.gz hg19 released duplicate lane review, biological replicates with identical biosample, missing derived_from insufficient read length ENCFF822FWM bed narrowPeak optimal idr thresholded peaks ENCSR000BKS ChIP-seq EFO:0002067 K562 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF697OMD, ENCFF713KSL, ENCFF847XRL 317644 ENCODE Processing Pipeline e0213c493c391ae380358cfc2d5a8490 https://www.encodeproject.org/files/ENCFF822FWM/@@download/ENCFF822FWM.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample control insufficient read depth, insufficient read depth, severe bottlenecking extremely low read depth, missing control alignments ENCFF768OPK bed narrowPeak optimal idr thresholded peaks ENCSR000AOA ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF474KGT, ENCFF652AZC, ENCFF915PWP 770935 ENCODE Processing Pipeline 37dbe73e85937bacc0dd37a6cd7e6353 https://www.encodeproject.org/files/ENCFF768OPK/@@download/ENCFF768OPK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity ENCFF222XPQ bed narrowPeak optimal idr thresholded peaks ENCSR000DZD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens EP300-human DNA False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF270RLY, ENCFF429WXC, ENCFF446MPR 352738 ENCODE Processing Pipeline d8641f789549a9b495f93565e6cf3260 https://www.encodeproject.org/files/ENCFF222XPQ/@@download/ENCFF222XPQ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent platforms, inconsistent target of control experiment ENCFF433PFN bed narrowPeak optimal idr thresholded peaks ENCSR000DYY ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens E2F4-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF128GGA, ENCFF191NQS, ENCFF319MWF 85609 ENCODE Processing Pipeline 62c04d74d3bb8393fd21d79f6d87f4c0 https://www.encodeproject.org/files/ENCFF433PFN/@@download/ENCFF433PFN.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF967ACD bed narrowPeak optimal idr thresholded peaks ENCSR000BNP ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF138XMK, ENCFF794ILD, ENCFF864PVD 602532 ENCODE Processing Pipeline a52540d0d7e72164a332058a082387ee https://www.encodeproject.org/files/ENCFF967ACD/@@download/ENCFF967ACD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF002DDA bed narrowPeak optimal idr thresholded peaks ENCSR000DUP ChIP-seq EFO:0002793 HL-60 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1 ENCFF001HOV 375499 ENCODE Consortium Analysis Working Group 2bc274678f574d811003c25e47864252 https://www.encodeproject.org/files/ENCFF002DDA/@@download/ENCFF002DDA.bed.gz hg19 released control low read depth, low read length, inconsistent platforms insufficient read depth ENCFF830KSV bed narrowPeak optimal idr thresholded peaks ENCSR000DUB ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF155SMN, ENCFF242KOJ, ENCFF263ZIY 629516 ENCODE Processing Pipeline e3851124fbda85eda9007e79e17f7d74 https://www.encodeproject.org/files/ENCFF830KSV/@@download/ENCFF830KSV.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth extremely low read depth, missing control alignments ENCFF747CHL bed narrowPeak optimal idr thresholded peaks ENCSR000BMZ ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ELF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF058SVD, ENCFF648CTU, ENCFF875YOA 363757 ENCODE Processing Pipeline 6cf30a6eafb808ec9250617a5b968d49 https://www.encodeproject.org/files/ENCFF747CHL/@@download/ENCFF747CHL.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF676YJE bed narrowPeak optimal idr thresholded peaks ENCSR000EGS ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 30.0 minute MYC-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF199SKV, ENCFF357NBU, ENCFF859MQB 636144 ENCODE Processing Pipeline ffdaabb82feb7296592767b1c23b26fa https://www.encodeproject.org/files/ENCFF676YJE/@@download/ENCFF676YJE.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample control insufficient read depth ENCFF002CMJ bed narrowPeak optimal idr thresholded peaks ENCSR000BGW ChIP-seq EFO:0002067 K562 cell line Homo sapiens SPI1-human DNA see document see document False 2011-07-18 ENCODE 551112 ENCODE Consortium Analysis Working Group e5deb59ab10ad4f9cf73e327a1094fd3 https://www.encodeproject.org/files/ENCFF002CMJ/@@download/ENCFF002CMJ.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF671RVI bed narrowPeak optimal idr thresholded peaks ENCSR000DRB ChIP-seq EFO:0005337 GM12864 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 3 ENCFF001TDO, ENCFF267DUF, ENCFF672SJH, ENCFF858HDY 739999 ENCODE Processing Pipeline aaf3b50473d1552c9b4cf0b4678f1564 https://www.encodeproject.org/files/ENCFF671RVI/@@download/ENCFF671RVI.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth missing raw data in replicate insufficient read depth missing control alignments ENCFF622GQO bed narrowPeak optimal idr thresholded peaks ENCSR000DKZ ChIP-seq EFO:0005345 GM13976 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF555GZI, ENCFF690YKI, ENCFF756RGK 519232 ENCODE Processing Pipeline 06def2b40abe0c2c60f7a804865ba3f7 https://www.encodeproject.org/files/ENCFF622GQO/@@download/ENCFF622GQO.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance biological replicates with identical biosample insufficient read depth control extremely low read depth, missing control alignments ENCFF462GHD bed narrowPeak optimal idr thresholded peaks ENCSR000DZG ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens EP300-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF632WHJ, ENCFF832BPN, ENCFF981IPY 297848 ENCODE Processing Pipeline d24dbbf4eb07c49cf63b19d7a03b606a https://www.encodeproject.org/files/ENCFF462GHD/@@download/ENCFF462GHD.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample control insufficient read depth, insufficient replicate concordance ENCFF319IEF bed narrowPeak optimal idr thresholded peaks ENCSR000EEE ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CEBPB-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF359DUK, ENCFF578MYY, ENCFF684XQE 898132 ENCODE Processing Pipeline 27ed624082593d867ab0b13fc13c0765 https://www.encodeproject.org/files/ENCFF319IEF/@@download/ENCFF319IEF.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF259JWD bed narrowPeak optimal idr thresholded peaks ENCSR000EDV ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens EP300-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF119LSM, ENCFF416FNH, ENCFF508ZEB 160207 ENCODE Processing Pipeline bb6fc9f0d80179bf7b4c03b16f98fb21 https://www.encodeproject.org/files/ENCFF259JWD/@@download/ENCFF259JWD.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CUD bed narrowPeak optimal idr thresholded peaks ENCSR000EET ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens forskolin and pyruvate 6.0 hour HSF1-human DNA see document see document False 2011-10-29 ENCODE 33058 ENCODE Consortium Analysis Working Group ac168e3835bf300e78e7f95c92016980 https://www.encodeproject.org/files/ENCFF002CUD/@@download/ENCFF002CUD.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF475MKH bed narrowPeak optimal idr thresholded peaks ENCSR000BQD ChIP-seq EFO:0001247 T47D cell line Homo sapiens bisphenol A 100.0 nM 30.0 minute ESR1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF355REI, ENCFF467HMZ, ENCFF716CEW 78926 ENCODE Processing Pipeline 56c17819f25811479adb57587a078f5e https://www.encodeproject.org/files/ENCFF475MKH/@@download/ENCFF475MKH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF331WKY bed narrowPeak optimal idr thresholded peaks ENCSR233FAG ChIP-seq EFO:0001184 HEK293T cell line Homo sapiens PKNOX1-human DNA False 2016-11-17 ENCODE 1, 2 ENCFF001TDO, ENCFF025FXN, ENCFF667IBC, ENCFF914KNX 838373 ENCODE Processing Pipeline d70bc76d79b6ddbf1d6f1726763db070 https://www.encodeproject.org/files/ENCFF331WKY/@@download/ENCFF331WKY.bed.gz hg19 released ENCFF079ZWK bed narrowPeak optimal idr thresholded peaks ENCSR000DZI ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MXI1-human DNA False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF603MKX, ENCFF711VHK, ENCFF776GTW 418493 ENCODE Processing Pipeline 6cacbee975f59501030c8b8587227808 https://www.encodeproject.org/files/ENCFF079ZWK/@@download/ENCFF079ZWK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, inconsistent target of control experiment ENCFF628QJU bed narrowPeak optimal idr thresholded peaks ENCSR000BRN ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFIC-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF019FNI, ENCFF729EFK, ENCFF806NEN 640810 ENCODE Processing Pipeline dc9ce027a41e9f4547f9aa222c71c62c https://www.encodeproject.org/files/ENCFF628QJU/@@download/ENCFF628QJU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity biological replicates with identical biosample ENCFF933VBD bed narrowPeak optimal idr thresholded peaks ENCSR000DUX ChIP-seq CL:0002557 fibroblast of pulmonary artery primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF470ARY, ENCFF541OOY, ENCFF610GLP 739247 ENCODE Processing Pipeline a0ca7418cb4781ded156ca6489564a8e https://www.encodeproject.org/files/ENCFF933VBD/@@download/ENCFF933VBD.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms missing control alignments ENCFF809ECY bed narrowPeak optimal idr thresholded peaks ENCSR000BJO ChIP-seq EFO:0002713 Panc1 cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF010OHK, ENCFF343XMY, ENCFF806MDV 130269 ENCODE Processing Pipeline 399777c2cb290a54d476ab74c5d32b5c https://www.encodeproject.org/files/ENCFF809ECY/@@download/ENCFF809ECY.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF459DRJ bed narrowPeak optimal idr thresholded peaks ENCSR000BMC ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens HDAC2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF380BKK, ENCFF561VAE, ENCFF724UMT 459887 ENCODE Processing Pipeline c7902bf5a399621d8bc456b6fcbdcae4 https://www.encodeproject.org/files/ENCFF459DRJ/@@download/ENCFF459DRJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample ENCFF716LRI bed narrowPeak optimal idr thresholded peaks ENCSR000EGO ChIP-seq EFO:0002067 K562 cell line Homo sapiens RFX5-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF066GNV, ENCFF439SZI, ENCFF536YVV 52639 ENCODE Processing Pipeline 175fa8254c3ee7f766ed461e264093dd https://www.encodeproject.org/files/ENCFF716LRI/@@download/ENCFF716LRI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF132AJR bed narrowPeak optimal idr thresholded peaks ENCSR000DRE ChIP-seq EFO:0005338 GM12865 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 2, 3 ENCFF001TDO, ENCFF109JHW, ENCFF583NIC, ENCFF867NAA 606092 ENCODE Processing Pipeline c933cf05e523d56a4937c4b313fc01ea https://www.encodeproject.org/files/ENCFF132AJR/@@download/ENCFF132AJR.bed.gz hg19 released control low read depth, low read length, low read depth, inconsistent platforms missing raw data in replicate insufficient read depth missing control alignments ENCFF210PLK bed narrowPeak optimal idr thresholded peaks ENCSR000DKP ChIP-seq EFO:0005334 GM10248 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF049XKA, ENCFF251JON, ENCFF927PCL 563417 ENCODE Processing Pipeline e0ba950f98c4bcacedd5503af90fa466 https://www.encodeproject.org/files/ENCFF210PLK/@@download/ENCFF210PLK.bed.gz hg19 released mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth control extremely low read depth, missing control alignments ENCFF659WGE bed narrowPeak optimal idr thresholded peaks ENCSR000EWM ChIP-seq EFO:0002067 K562 cell line Homo sapiens GATA1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF281ONW, ENCFF830VFD, ENCFF942MUF 69686 ENCODE Processing Pipeline 1173386ed1cdefa8840fec380d4ffbde https://www.encodeproject.org/files/ENCFF659WGE/@@download/ENCFF659WGE.bed.gz hg19 released borderline replicate concordance biological replicates with identical biosample insufficient read depth, insufficient read length extremely low read depth ENCFF950LQM bed narrowPeak optimal idr thresholded peaks ENCSR000EZD ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MYC-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF045UZK, ENCFF224GZD, ENCFF471HJA 209438 ENCODE Processing Pipeline 9c585bf7485ac45eac9214d50fa11e73 https://www.encodeproject.org/files/ENCFF950LQM/@@download/ENCFF950LQM.bed.gz hg19 released control low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth, insufficient read length extremely low read depth ENCFF533NIV bed narrowPeak optimal idr thresholded peaks ENCSR000BPT ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour ELF1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF200DAE, ENCFF386WPS, ENCFF731JIX 201656 ENCODE Processing Pipeline 8235e20c036071844e126474e0b8d102 https://www.encodeproject.org/files/ENCFF533NIV/@@download/ENCFF533NIV.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF903ZMF bed narrowPeak optimal idr thresholded peaks ENCSR000BNO ChIP-seq EFO:0001247 T47D cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour CTCF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF885ILM, ENCFF976NKK, ENCFF986CUM 482518 ENCODE Processing Pipeline 765dd9a4fdebd8971d21488e7b273e3a https://www.encodeproject.org/files/ENCFF903ZMF/@@download/ENCFF903ZMF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF673PTK bed narrowPeak optimal idr thresholded peaks ENCSR000EIB ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens JUND-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF398EYK, ENCFF413ZYK, ENCFF830ZWP 555908 ENCODE Processing Pipeline 152128b76890ff621885ed224a0216df https://www.encodeproject.org/files/ENCFF673PTK/@@download/ENCFF673PTK.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF738TKN bed narrowPeak optimal idr thresholded peaks ENCSR000EGM ChIP-seq EFO:0002067 K562 cell line Homo sapiens CTCF-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF264LXL, ENCFF545EHA, ENCFF595QHF 905102 ENCODE Processing Pipeline 8635b84f3c5785702257302d4b4b8f8a https://www.encodeproject.org/files/ENCFF738TKN/@@download/ENCFF738TKN.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment biological replicates with identical biosample ENCFF718CQQ bed narrowPeak optimal idr thresholded peaks ENCSR000EEB ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MAFK-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF016LSH, ENCFF067XYR, ENCFF092FFG 1231199 ENCODE Processing Pipeline c064056c9a2aee65e331abb72aa9a0e8 https://www.encodeproject.org/files/ENCFF718CQQ/@@download/ENCFF718CQQ.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF598VEK bed narrowPeak optimal idr thresholded peaks ENCSR525YFS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZBTB40-human DNA False 2016-08-01 ENCODE 1, 2 ENCFF001TDO, ENCFF246GJS, ENCFF741YYS, ENCFF829CKQ 120849 ENCODE Processing Pipeline caa96ece080332e78a21cb467dfbe8d6 https://www.encodeproject.org/files/ENCFF598VEK/@@download/ENCFF598VEK.bed.gz hg19 released antibody characterized with exemption ENCFF891MVM bed narrowPeak optimal idr thresholded peaks ENCSR000EWN ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZNF263-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF051FKL, ENCFF100FXA, ENCFF537UES 67975 ENCODE Processing Pipeline 6f1947b757a7ffc01cf96e02420dce62 https://www.encodeproject.org/files/ENCFF891MVM/@@download/ENCFF891MVM.bed.gz hg19 released biological replicates with identical biosample insufficient read length extremely low read depth ENCFF822SAU bed narrowPeak optimal idr thresholded peaks ENCSR000EVW ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens GATA2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF222CSK, ENCFF311XFB, ENCFF991EAY 506227 ENCODE Processing Pipeline b147b14daf5660d3097f5ce840d9be19 https://www.encodeproject.org/files/ENCFF822SAU/@@download/ENCFF822SAU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF297HAT bed narrowPeak optimal idr thresholded peaks ENCSR000BPU ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour ETS1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF276JRH, ENCFF394JUH, ENCFF998WPB 180375 ENCODE Processing Pipeline bf0caaa46405e97b31b7ab3ec0c68245 https://www.encodeproject.org/files/ENCFF297HAT/@@download/ENCFF297HAT.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample ENCFF002CRQ bed narrowPeak optimal idr thresholded peaks ENCSR000EVD ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens ZNF263-human DNA see document see document False 2011-10-29 ENCODE 624271 ENCODE Consortium Analysis Working Group d303f02a1d97ffeca6956990ab0c9ed0 https://www.encodeproject.org/files/ENCFF002CRQ/@@download/ENCFF002CRQ.bed.gz hg19 released low read length, low read depth, mixed read lengths biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CXH bed narrowPeak optimal idr thresholded peaks ENCSR000FAF ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFE2-human DNA see document see document False 2011-10-29 ENCODE 53709 ENCODE Consortium Analysis Working Group 3fa5b2aaff7064f6bb43628c6a33c4a5 https://www.encodeproject.org/files/ENCFF002CXH/@@download/ENCFF002CXH.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF335GSE bed narrowPeak optimal idr thresholded peaks ENCSR000AUE ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 100 nM 1 hour CTCF-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF014XSY, ENCFF142SVH, ENCFF781ICW 934065 ENCODE Processing Pipeline 1d3fadf80cf68565771e62c429c76195 https://www.encodeproject.org/files/ENCFF335GSE/@@download/ENCFF335GSE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF199FYD bed narrowPeak optimal idr thresholded peaks ENCSR000BHJ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens PAX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF194IYQ, ENCFF735NFJ, ENCFF906INE 384049 ENCODE Processing Pipeline 07b55f11fdb125a63ab500f783d05d7b https://www.encodeproject.org/files/ENCFF199FYD/@@download/ENCFF199FYD.bed.gz hg19 released low read length, borderline replicate concordance, low read depth biological replicates with identical biosample insufficient read depth ENCFF369JAI bed narrowPeak optimal idr thresholded peaks ENCSR000BJW ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens RXRA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF673CDR, ENCFF701HCP, ENCFF914ZYY 35031 ENCODE Processing Pipeline 45eac8a6717368c2995378b49497d131 https://www.encodeproject.org/files/ENCFF369JAI/@@download/ENCFF369JAI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF002CVE bed narrowPeak optimal idr thresholded peaks ENCSR000EEZ ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens MAX-human DNA see document see document False 2011-10-29 ENCODE 202694 ENCODE Consortium Analysis Working Group 49d2220b47726f1448c459b0c7fdb9f0 https://www.encodeproject.org/files/ENCFF002CVE/@@download/ENCFF002CVE.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF002DAX bed narrowPeak optimal idr thresholded peaks ENCSR000DLS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 754913 ENCODE Consortium Analysis Working Group ecbae2a248b1e92b1f5eb99c8d762a63 https://www.encodeproject.org/files/ENCFF002DAX/@@download/ENCFF002DAX.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF243NQJ bed narrowPeak optimal idr thresholded peaks ENCSR000DYI ChIP-seq EFO:0001086 A549 cell line Homo sapiens CEBPB-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF488XZE, ENCFF694VSV, ENCFF710XFQ 820421 ENCODE Processing Pipeline eba9d012ffcc64edd76e443df53f3662 https://www.encodeproject.org/files/ENCFF243NQJ/@@download/ENCFF243NQJ.bed.gz hg19 released low read length, low read depth, inconsistent platforms, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CJR bed narrowPeak optimal idr thresholded peaks ENCSR000BRY ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens TEAD4-human DNA see document see document False 2012-09-10 ENCODE 409026 ENCODE Consortium Analysis Working Group c852448911067252d6b3be1e7ea922d5 https://www.encodeproject.org/files/ENCFF002CJR/@@download/ENCFF002CJR.bed.gz hg19 released low read length, inconsistent platforms, mixed read lengths biological replicates with identical biosample, missing derived_from ENCFF849EEH bed narrowPeak optimal idr thresholded peaks ENCSR000EHY ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens RFX5-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF668SRV, ENCFF695DKI, ENCFF860WKG 158174 ENCODE Processing Pipeline 37f5f64bc9fc3481a401537dd3e2b6f8 https://www.encodeproject.org/files/ENCFF849EEH/@@download/ENCFF849EEH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF594LCH bed narrowPeak optimal idr thresholded peaks ENCSR000EWH ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR2C2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF342EJU, ENCFF837CQV, ENCFF841ZNM 11703 ENCODE Processing Pipeline b644a99d8801abfd2155e186effd31ba https://www.encodeproject.org/files/ENCFF594LCH/@@download/ENCFF594LCH.bed.gz hg19 released biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF612TRG bed narrowPeak optimal idr thresholded peaks ENCSR521IID ChIP-seq UBERON:0002107 liver tissue Homo sapiens MAX-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF137BQM, ENCFF371DUN, ENCFF409TGM 593414 ENCODE Processing Pipeline 4f8617bfcdcb64e666fd3bea1450f25e https://www.encodeproject.org/files/ENCFF612TRG/@@download/ENCFF612TRG.bed.gz hg19 released antibody characterized with exemption biological replicates with identical biosample ENCFF930QUM bed narrowPeak optimal idr thresholded peaks ENCSR000DQW ChIP-seq EFO:0002783 GM06990 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF174YEU, ENCFF276JDQ, ENCFF830SNU 736511 ENCODE Processing Pipeline bd61a515467d59a908d9e5668b3e868e https://www.encodeproject.org/files/ENCFF930QUM/@@download/ENCFF930QUM.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms insufficient read depth, poor library complexity, severe bottlenecking ENCFF672FQU bed narrowPeak optimal idr thresholded peaks ENCSR000BQQ ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour TCF12-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF396UAX, ENCFF842BMF, ENCFF866QPM 537307 ENCODE Processing Pipeline 4efdaea798e890432a3edc08cd6cb780 https://www.encodeproject.org/files/ENCFF672FQU/@@download/ENCFF672FQU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF002DAZ bed narrowPeak optimal idr thresholded peaks ENCSR000DLU ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens MYC-human DNA see document see document False 2011-03-17 ENCODE 98320 ENCODE Consortium Analysis Working Group ed57885cdc2e621df9fe2934c4f4bd93 https://www.encodeproject.org/files/ENCFF002DAZ/@@download/ENCFF002DAZ.bed.gz hg19 released low read length, mild to moderate bottlenecking missing derived_from insufficient read depth ENCFF881EJW bed narrowPeak optimal idr thresholded peaks ENCSR085IXF ChIP-seq UBERON:0002107 liver tissue Homo sapiens SP1-human DNA False 2018-02-08 ENCODE 1, 2 ENCFF001TDO, ENCFF204PED, ENCFF502LWJ, ENCFF512BFW 1278434 ENCODE Processing Pipeline 9db9e2a5dead65918863cdd899a150cd https://www.encodeproject.org/files/ENCFF881EJW/@@download/ENCFF881EJW.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample, experiment not submitted to GEO ENCFF113PMT bed narrowPeak optimal idr thresholded peaks ENCSR000EGQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFYB-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF180NNF, ENCFF193FRQ, ENCFF570JVX 159170 ENCODE Processing Pipeline 17bb2e1d538afdee207dfa2b58c5fa95 https://www.encodeproject.org/files/ENCFF113PMT/@@download/ENCFF113PMT.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read length extremely low read depth ENCFF975PTM bed narrowPeak optimal idr thresholded peaks ENCSR480LIS ChIP-seq UBERON:0002107 liver tissue Homo sapiens ATF3-human DNA False 2016-03-31 ENCODE 1, 2 ENCFF001TDO, ENCFF189KUR, ENCFF770XDD, ENCFF788BDL 419388 ENCODE Processing Pipeline a00b36b1c73079054c5df7c5d21b322e https://www.encodeproject.org/files/ENCFF975PTM/@@download/ENCFF975PTM.bed.gz hg19 released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF931XAL bed narrowPeak optimal idr thresholded peaks ENCSR000DZO ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NRF1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF502JYT, ENCFF562LQW, ENCFF789TQP 90284 ENCODE Processing Pipeline 49b2701b7ddb6de70c1f665a1d884702 https://www.encodeproject.org/files/ENCFF931XAL/@@download/ENCFF931XAL.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CSD bed narrowPeak optimal idr thresholded peaks ENCSR000EDG ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens JUN-human DNA see document see document False 2011-10-29 ENCODE 540407 ENCODE Consortium Analysis Working Group 48b2d8533a6c3c059d9939f1cc1964cc https://www.encodeproject.org/files/ENCFF002CSD/@@download/ENCFF002CSD.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CTR bed narrowPeak optimal idr thresholded peaks ENCSR000DNT ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZZZ3-human DNA see document see document False 2011-10-29 ENCODE 7257 ENCODE Consortium Analysis Working Group 7695f41be364380f1e726d98727cc044 https://www.encodeproject.org/files/ENCFF002CTR/@@download/ENCFF002CTR.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample, missing derived_from ENCFF280GDT bed narrowPeak optimal idr thresholded peaks ENCSR000BTK ChIP-seq EFO:0002793 HL-60 cell line Homo sapiens GABPA-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF148CAJ, ENCFF647DHT, ENCFF847KJV 165440 ENCODE Processing Pipeline 703045c5651246291956c1efe81a8e2e https://www.encodeproject.org/files/ENCFF280GDT/@@download/ENCFF280GDT.bed.gz hg19 released low read depth biological replicates with identical biosample ENCFF739PUT bed narrowPeak optimal idr thresholded peaks ENCSR016BMM ChIP-seq UBERON:0002107 liver tissue Homo sapiens TAF1-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF225XDH, ENCFF407JBN, ENCFF903KIH 240640 ENCODE Processing Pipeline 0de78ae36c8572df537336ab5bdb9f6d https://www.encodeproject.org/files/ENCFF739PUT/@@download/ENCFF739PUT.bed.gz hg19 released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF205YOD bed narrowPeak optimal idr thresholded peaks ENCSR000EBP ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens GTF2F1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF211BEL, ENCFF258FIQ, ENCFF449PNR 77008 ENCODE Processing Pipeline c922c340580a815e7117f367dda72e7b https://www.encodeproject.org/files/ENCFF205YOD/@@download/ENCFF205YOD.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF468MFY bed narrowPeak optimal idr thresholded peaks ENCSR000BHA ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BCL11A-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF046PLS, ENCFF080MVF, ENCFF289FQM 345367 ENCODE Processing Pipeline 7f180aca1612b6d01a7e549b1e685303 https://www.encodeproject.org/files/ENCFF468MFY/@@download/ENCFF468MFY.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF325WAV bed narrowPeak optimal idr thresholded peaks ENCSR000BQH ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour BCL3-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF395ZTW, ENCFF464UMR, ENCFF746BWA 232452 ENCODE Processing Pipeline 0842e3bc3cde1110bda1860a4a18a8fc https://www.encodeproject.org/files/ENCFF325WAV/@@download/ENCFF325WAV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF364QXM bed narrowPeak optimal idr thresholded peaks ENCSR000DTO ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF498JUY, ENCFF655DUF, ENCFF988DJT 813755 ENCODE Processing Pipeline 28ab0b38761553ef323901ac055b31f4 https://www.encodeproject.org/files/ENCFF364QXM/@@download/ENCFF364QXM.bed.gz hg19 released control low read depth, low read length, low read depth ENCFF793BVO bed narrowPeak optimal idr thresholded peaks ENCSR000BHS ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens GABPA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF428HJN, ENCFF588CWW, ENCFF985GJY 134074 ENCODE Processing Pipeline 3b852f9fa019239b89ab2631c48a10a8 https://www.encodeproject.org/files/ENCFF793BVO/@@download/ENCFF793BVO.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF002CRV bed narrowPeak optimal idr thresholded peaks ENCSR000DNX ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens BDP1-human DNA see document see document False 2011-10-29 ENCODE 13232 ENCODE Consortium Analysis Working Group fe274615f1addff9d92690272a00fbc4 https://www.encodeproject.org/files/ENCFF002CRV/@@download/ENCFF002CRV.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF684BLN bed narrowPeak optimal idr thresholded peaks ENCSR000BGM ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens USF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF308DEQ, ENCFF316GUJ, ENCFF805TIZ 400681 ENCODE Processing Pipeline 3899b7d76e13cf4087901a7fac9fddb1 https://www.encodeproject.org/files/ENCFF684BLN/@@download/ENCFF684BLN.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF002CWC bed narrowPeak optimal idr thresholded peaks ENCSR000FAH ChIP-seq EFO:0002067 K562 cell line Homo sapiens JUN-human DNA see document see document False 2011-10-29 ENCODE 192247 ENCODE Consortium Analysis Working Group abdba0bac5cb6444fefa32850edddc63 https://www.encodeproject.org/files/ENCFF002CWC/@@download/ENCFF002CWC.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF344EDE bed narrowPeak optimal idr thresholded peaks ENCSR080XEY ChIP-seq UBERON:0002107 liver tissue Homo sapiens FOXA2-human DNA False 2016-06-30 ENCODE 1, 2 ENCFF001TDO, ENCFF216JDJ, ENCFF539QIT, ENCFF555YAB 474546 ENCODE Processing Pipeline d3e6b822f6c76b83e10faeeac4e38d0c https://www.encodeproject.org/files/ENCFF344EDE/@@download/ENCFF344EDE.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity, antibody characterized with exemption biological replicates with identical biosample ENCFF160WLU bed narrowPeak optimal idr thresholded peaks ENCSR000BGZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TCF12-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF571QYV, ENCFF734EMB, ENCFF814CGS 441776 ENCODE Processing Pipeline 1de50ea947fc32b20c14525ecf1087ac https://www.encodeproject.org/files/ENCFF160WLU/@@download/ENCFF160WLU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF516GZM bed narrowPeak optimal idr thresholded peaks ENCSR000BJS ChIP-seq EFO:0001247 T47D cell line Homo sapiens genistein 100 nM 1 hour ESR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF198ZBJ, ENCFF421BMH, ENCFF785UNT 208549 ENCODE Processing Pipeline 27aebe53e5af34c047820fe32f992ef1 https://www.encodeproject.org/files/ENCFF516GZM/@@download/ENCFF516GZM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF245PXW bed narrowPeak optimal idr thresholded peaks ENCSR000DPS ChIP-seq NTR:0000480 AG09319 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF053EST, ENCFF528DMI, ENCFF949AFF 631971 ENCODE Processing Pipeline 962745b1d6d487ac2007f2d725ee8996 https://www.encodeproject.org/files/ENCFF245PXW/@@download/ENCFF245PXW.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity NTR biosample ENCFF002CSH bed narrowPeak optimal idr thresholded peaks ENCSR000EVL ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens E2F4-human DNA see document see document False 2011-10-29 ENCODE 72250 ENCODE Consortium Analysis Working Group b0ee76b4bd597ffc28d3fbb455b4bca8 https://www.encodeproject.org/files/ENCFF002CSH/@@download/ENCFF002CSH.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF913WFD bed narrowPeak optimal idr thresholded peaks ENCSR000BHG ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 5 nM 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF012IVJ, ENCFF055UFA, ENCFF457IQL 226305 ENCODE Processing Pipeline 7c2d8a1c2786b19864e7a6e535d292ce https://www.encodeproject.org/files/ENCFF913WFD/@@download/ENCFF913WFD.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CUY bed narrowPeak optimal idr thresholded peaks ENCSR000EVS ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens NR2C2-human DNA see document see document False 2011-10-29 ENCODE 68743 ENCODE Consortium Analysis Working Group 1341c254fe193f8e1b74e523a83b53fb https://www.encodeproject.org/files/ENCFF002CUY/@@download/ENCFF002CUY.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF799HIG bed narrowPeak optimal idr thresholded peaks ENCSR000EFV ChIP-seq EFO:0002067 K562 cell line Homo sapiens MAX-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF087MNA, ENCFF375JMY, ENCFF417GYT 624145 ENCODE Processing Pipeline 1b006f9e5ad27a54abb8329a52edd9d8 https://www.encodeproject.org/files/ENCFF799HIG/@@download/ENCFF799HIG.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF002CWI bed narrowPeak optimal idr thresholded peaks ENCSR000FAG ChIP-seq EFO:0002067 K562 cell line Homo sapiens MYC-human DNA see document see document False 2011-10-29 ENCODE 100566 ENCODE Consortium Analysis Working Group dc7b2f11aa6ce545fdba1c08dc21c233 https://www.encodeproject.org/files/ENCFF002CWI/@@download/ENCFF002CWI.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF402FYF bed narrowPeak optimal idr thresholded peaks ENCSR000DZW ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RFX5-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF381NIE, ENCFF628ZZL, ENCFF868UJU 110449 ENCODE Processing Pipeline 811017cf274710fe6aaf8c06d8649580 https://www.encodeproject.org/files/ENCFF402FYF/@@download/ENCFF402FYF.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF420KEV bed narrowPeak optimal idr thresholded peaks ENCSR000BNT ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF224GWF, ENCFF387XCG, ENCFF725GND 399156 ENCODE Processing Pipeline 88ed7aa67f32ef173648f7033515b4f7 https://www.encodeproject.org/files/ENCFF420KEV/@@download/ENCFF420KEV.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF902CVS bed narrowPeak optimal idr thresholded peaks ENCSR000BNR ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens HDAC2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF159YRA, ENCFF273RCZ, ENCFF536YJT 183886 ENCODE Processing Pipeline 3f3592fa333e52b9cca1baa9811787c8 https://www.encodeproject.org/files/ENCFF902CVS/@@download/ENCFF902CVS.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample ENCFF766ERZ bed narrowPeak optimal idr thresholded peaks ENCSR000DZY ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens NFE2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF126LPK, ENCFF168WPY, ENCFF955NAK 2372 ENCODE Processing Pipeline 95644ae74fe0934d417696338f134eae https://www.encodeproject.org/files/ENCFF766ERZ/@@download/ENCFF766ERZ.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample control insufficient read depth ENCFF964BYN bed narrowPeak optimal idr thresholded peaks ENCSR000EBW ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens ZNF143-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF080SVL, ENCFF180SZJ, ENCFF902CAT 639247 ENCODE Processing Pipeline cca4fd168c13d68f7e9751c2a7a43c7c https://www.encodeproject.org/files/ENCFF964BYN/@@download/ENCFF964BYN.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF964JXI bed narrowPeak optimal idr thresholded peaks ENCSR000BHU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens RXRA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF679VQP, ENCFF915JCV, ENCFF976ZDJ 425321 ENCODE Processing Pipeline d540c903680e4b4ac7aea04e684324a5 https://www.encodeproject.org/files/ENCFF964JXI/@@download/ENCFF964JXI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient replicate concordance missing control alignments ENCFF016EUX bed narrowPeak optimal idr thresholded peaks ENCSR000DYB ChIP-seq EFO:0001260 WI38 cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF200KQQ, ENCFF381HQF, ENCFF658PRB 489043 ENCODE Processing Pipeline 3b4175ee806d5059eb5007e4fa19891b https://www.encodeproject.org/files/ENCFF016EUX/@@download/ENCFF016EUX.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking insufficient read depth ENCFF290HTJ bed narrowPeak optimal idr thresholded peaks ENCSR000FAV ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 30.0 minute STAT1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF490WRP, ENCFF622FPS, ENCFF695SDJ 25619 ENCODE Processing Pipeline a9aa20b61b6e61db5f4a49be039c6f10 https://www.encodeproject.org/files/ENCFF290HTJ/@@download/ENCFF290HTJ.bed.gz hg19 released control low read depth biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF002CSU bed narrowPeak optimal idr thresholded peaks ENCSR000DNS ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens NFYA-human DNA see document see document False 2011-10-29 ENCODE 145549 ENCODE Consortium Analysis Working Group 0648b23890a30a1df457a5ccd1b72a85 https://www.encodeproject.org/files/ENCFF002CSU/@@download/ENCFF002CSU.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF048OBR bed narrowPeak optimal idr thresholded peaks ENCSR000EGA ChIP-seq EFO:0002067 K562 cell line Homo sapiens TBL1XR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF029WBH, ENCFF148FBK, ENCFF570BGF 116170 ENCODE Processing Pipeline af849a8e32cce9ef81c5076327bc52fa https://www.encodeproject.org/files/ENCFF048OBR/@@download/ENCFF048OBR.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF070SAY bed narrowPeak optimal idr thresholded peaks ENCSR000BQN ChIP-seq EFO:0005234 PFSK-1 cell line Homo sapiens TAF1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF499YNQ, ENCFF652LUF, ENCFF854IEG 277003 ENCODE Processing Pipeline 1a8073f1f951fdd5f174cb43a8608abf https://www.encodeproject.org/files/ENCFF070SAY/@@download/ENCFF070SAY.bed.gz hg19 released control low read depth, low read length, borderline replicate concordance biological replicates with identical biosample insufficient read depth ENCFF415WKV bed narrowPeak optimal idr thresholded peaks ENCSR000AOO ChIP-seq CL:0000127 astrocyte primary cell Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF113DAW, ENCFF527FXX, ENCFF857XBX 576020 ENCODE Processing Pipeline 86f81256e7eb31e31845b1b9a9c45e35 https://www.encodeproject.org/files/ENCFF415WKV/@@download/ENCFF415WKV.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity NTR biosample insufficient read depth ENCFF002DCF bed narrowPeak optimal idr thresholded peaks ENCSR000DQY ChIP-seq EFO:0005353 GM12801 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1 ENCFF001HBB 54731 ENCODE Consortium Analysis Working Group 596392705bd0e7954538494d7f40be01 https://www.encodeproject.org/files/ENCFF002DCF/@@download/ENCFF002DCF.bed.gz hg19 released control low read depth inconsistent mapped reads lengths insufficient read length extremely low read depth ENCFF002CPK bed narrowPeak optimal idr thresholded peaks ENCSR000EAC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RAD21-human DNA see document see document False 2011-10-29 ENCODE 757929 ENCODE Consortium Analysis Working Group 90be6eca516f3df86ba962066a7b0f55 https://www.encodeproject.org/files/ENCFF002CPK/@@download/ENCFF002CPK.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CRX bed narrowPeak optimal idr thresholded peaks ENCSR000DNW ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens BRF1-human DNA see document see document False 2011-10-29 ENCODE 5388 ENCODE Consortium Analysis Working Group 2281830d1b316504434057ff8956cf29 https://www.encodeproject.org/files/ENCFF002CRX/@@download/ENCFF002CRX.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF390MXI bed narrowPeak optimal idr thresholded peaks ENCSR000EVU ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens FOS-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF221BNG, ENCFF387HZM, ENCFF587UQZ 768034 ENCODE Processing Pipeline c6480e664f94e84cc9968f1178d9c24b https://www.encodeproject.org/files/ENCFF390MXI/@@download/ENCFF390MXI.bed.gz hg19 released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity biological replicates with identical biosample, duplicate lane review insufficient read depth ENCFF553PWA bed narrowPeak optimal idr thresholded peaks ENCSR000BLE ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens FOXA1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF157CCV, ENCFF169DCU, ENCFF245NLP 926013 ENCODE Processing Pipeline 3400c823c9ffb82c25a3addbaa5fa42a https://www.encodeproject.org/files/ENCFF553PWA/@@download/ENCFF553PWA.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF276MQI bed narrowPeak optimal idr thresholded peaks ENCSR000BIZ ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour ESR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF451WEI, ENCFF630EHJ, ENCFF775ACP 51885 ENCODE Processing Pipeline 300a8deab5912d00fca9e4eb3e75031a https://www.encodeproject.org/files/ENCFF276MQI/@@download/ENCFF276MQI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth missing control alignments ENCFF358BEF bed narrowPeak optimal idr thresholded peaks ENCSR000BIU ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens USF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF074EWX, ENCFF433NME, ENCFF868HHE 527733 ENCODE Processing Pipeline 3094c785a738fc27832b7fe913c3d950 https://www.encodeproject.org/files/ENCFF358BEF/@@download/ENCFF358BEF.bed.gz hg19 released low read length, low read depth biological replicates with identical biosample ENCFF264LQE bed narrowPeak optimal idr thresholded peaks ENCSR000BQA ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens ZBTB7A-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF525ETQ, ENCFF598OWM, ENCFF973ZCY 225076 ENCODE Processing Pipeline 7ceb1eb4f2ead35aceb6dac50379a772 https://www.encodeproject.org/files/ENCFF264LQE/@@download/ENCFF264LQE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF002CLP bed narrowPeak optimal idr thresholded peaks ENCSR000BKH ChIP-seq EFO:0002067 K562 cell line Homo sapiens BCLAF1-human DNA see document see document False 2011-07-18 ENCODE 87373 ENCODE Consortium Analysis Working Group 84b23b96b527536feaeb011ecb3ad402 https://www.encodeproject.org/files/ENCFF002CLP/@@download/ENCFF002CLP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, mixed read lengths biological replicates with identical biosample, missing derived_from control insufficient read depth ENCFF203EDM bed narrowPeak optimal idr thresholded peaks ENCSR000BKH ChIP-seq EFO:0002067 K562 cell line Homo sapiens BCLAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF185HLZ, ENCFF650YKB, ENCFF674BPH 40925 ENCODE Processing Pipeline 3946dde3684d502243421593940f2481 https://www.encodeproject.org/files/ENCFF203EDM/@@download/ENCFF203EDM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, mixed read lengths biological replicates with identical biosample control insufficient read depth ENCFF002CRY bed narrowPeak optimal idr thresholded peaks ENCSR000DNV ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens BRF2-human DNA see document see document False 2011-10-29 ENCODE 8295 ENCODE Consortium Analysis Working Group 9398a1a6df6864705eb7fae3e09199ef https://www.encodeproject.org/files/ENCFF002CRY/@@download/ENCFF002CRY.bed.gz hg19 released inconsistent platforms biological replicates with identical biosample, missing derived_from insufficient read length ENCFF957YRU bed narrowPeak optimal idr thresholded peaks ENCSR000DYZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TBL1XR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF453YFD, ENCFF630PWI, ENCFF941AZB 297607 ENCODE Processing Pipeline 5e70a5136c41813c1a7f9b17b00685f4 https://www.encodeproject.org/files/ENCFF957YRU/@@download/ENCFF957YRU.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF648NYF bed narrowPeak optimal idr thresholded peaks ENCSR000EHJ ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 6.0 hour STAT1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF473ULH, ENCFF797EKN, ENCFF947WYS 49746 ENCODE Processing Pipeline 2a8c734f74b99e36c8be46d2216ac62e https://www.encodeproject.org/files/ENCFF648NYF/@@download/ENCFF648NYF.bed.gz hg19 released control low read depth, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF508IBP bed narrowPeak optimal idr thresholded peaks ENCSR000ECC ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens NRF1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF392HAM, ENCFF547PLM, ENCFF987TTM 87681 ENCODE Processing Pipeline 665542539f7b759c7b820632d8d8d8c3 https://www.encodeproject.org/files/ENCFF508IBP/@@download/ENCFF508IBP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF772XQF bed narrowPeak optimal idr thresholded peaks ENCSR000ARO ChIP-seq CL:0002553 fibroblast of lung primary cell Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF013CEU, ENCFF306KIF, ENCFF379HMO 243525 ENCODE Processing Pipeline e318abb26c13b0c4841f1a0da0747386 https://www.encodeproject.org/files/ENCFF772XQF/@@download/ENCFF772XQF.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking missing control alignments ENCFF689AXJ bed narrowPeak optimal idr thresholded peaks ENCSR000DYV ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MAFK-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF122PLB, ENCFF156VOX, ENCFF226PAC 121444 ENCODE Processing Pipeline b61b43061a198f6f74206eee7d7b8e4a https://www.encodeproject.org/files/ENCFF689AXJ/@@download/ENCFF689AXJ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample, inconsistent mapped reads lengths ENCFF134XDY bed narrowPeak optimal idr thresholded peaks ENCSR251OVJ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SMAD5-human DNA False 2016-02-02 ENCODE 1, 2 ENCFF001TDO, ENCFF045XQS, ENCFF502RRE, ENCFF895ECZ 206496 ENCODE Processing Pipeline d8344e811dbec6f17020acdb4a272fc5 https://www.encodeproject.org/files/ENCFF134XDY/@@download/ENCFF134XDY.bed.gz hg19 released low read depth, antibody characterized with exemption ENCFF677OWM bed narrowPeak optimal idr thresholded peaks ENCSR996ESX ChIP-seq EFO:0002067 K562 cell line Homo sapiens NFRKB-human DNA False 2018-01-26 ENCODE 1, 2 ENCFF001TDO, ENCFF139EAR, ENCFF630SOG, ENCFF648NVD 149805 ENCODE Processing Pipeline a3af5e542702471717992287eaae5b71 https://www.encodeproject.org/files/ENCFF677OWM/@@download/ENCFF677OWM.bed.gz hg19 released mild to moderate bottlenecking, low read depth experiment not submitted to GEO partially characterized antibody ENCFF473GCH bed narrowPeak optimal idr thresholded peaks ENCSR000BMV ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOSL1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF400JWL, ENCFF753OLX, ENCFF818IMH 133495 ENCODE Processing Pipeline 86ddcb80bb8c5f873e909777fd5562ce https://www.encodeproject.org/files/ENCFF473GCH/@@download/ENCFF473GCH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample control insufficient read depth ENCFF002CUC bed narrowPeak optimal idr thresholded peaks ENCSR000EEU ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens forskolin and pyruvate 6.0 hour HNF4A-human DNA see document see document False 2011-10-29 ENCODE 213158 ENCODE Consortium Analysis Working Group 006988cb6eb478daf34722128c086ab7 https://www.encodeproject.org/files/ENCFF002CUC/@@download/ENCFF002CUC.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF082JDH bed narrowPeak optimal idr thresholded peaks ENCSR000DZS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens BRCA1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF093WNM, ENCFF106CWI, ENCFF443VLF 31791 ENCODE Processing Pipeline 10299328af6a1ef178cd4a17a91c4c3e https://www.encodeproject.org/files/ENCFF082JDH/@@download/ENCFF082JDH.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient replicate concordance ENCFF099SDW bed narrowPeak optimal idr thresholded peaks ENCSR000EZU ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 6.0 hour MYC-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF162CMX, ENCFF934ENB, ENCFF987HSI 365512 ENCODE Processing Pipeline a5ea998d3571ba34457f33fe6da76db2 https://www.encodeproject.org/files/ENCFF099SDW/@@download/ENCFF099SDW.bed.gz hg19 released control low read depth, borderline replicate concordance, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF660HHS bed narrowPeak optimal idr thresholded peaks ENCSR000DSZ ChIP-seq CL:0002603 astrocyte of the cerebellum primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF542XFE, ENCFF724RQI, ENCFF897VMF 765621 ENCODE Processing Pipeline 4c00b542348b145ccdfb55fee6c12ab9 https://www.encodeproject.org/files/ENCFF660HHS/@@download/ENCFF660HHS.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity insufficient read depth missing control alignments ENCFF453XKM bed narrowPeak optimal idr thresholded peaks ENCSR000EFI ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens CTCF-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF070OIO, ENCFF598QPN, ENCFF719YRP 749002 ENCODE Processing Pipeline 7012df7b06605f9a5fb69695e1a4178e https://www.encodeproject.org/files/ENCFF453XKM/@@download/ENCFF453XKM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample missing control alignments ENCFF336HCY bed narrowPeak optimal idr thresholded peaks ENCSR000ATS ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens SUZ12-human DNA see document see document False 2012-08-06 ENCODE 1, 3 ENCFF001TDO, ENCFF371ZTN, ENCFF588OJE, ENCFF907MBG 339267 ENCODE Processing Pipeline 8fce81d8aa02bb6084375e79f029bba9 https://www.encodeproject.org/files/ENCFF336HCY/@@download/ENCFF336HCY.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent platforms, mixed read lengths, moderate library complexity inconsistent mapped reads lengths ENCFF337WIE bed narrowPeak optimal idr thresholded peaks ENCSR000DWQ ChIP-seq CL:1001608 foreskin fibroblast primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF290QTC, ENCFF683BND, ENCFF947TJH 782984 ENCODE Processing Pipeline b3d90d4e894ae83cd81c99c55fc84db1 https://www.encodeproject.org/files/ENCFF337WIE/@@download/ENCFF337WIE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth missing control alignments ENCFF738CXX bed narrowPeak optimal idr thresholded peaks ENCSR000DVQ ChIP-seq CL:0002558 fibroblast of villous mesenchyme primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF232MQQ, ENCFF569PZS, ENCFF883QKB 768494 ENCODE Processing Pipeline 5a3c9d8e93fc9918892fa2f3ecf1426a https://www.encodeproject.org/files/ENCFF738CXX/@@download/ENCFF738CXX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth insufficient read depth ENCFF422NGZ bed narrowPeak optimal idr thresholded peaks ENCSR000BLP ChIP-seq EFO:0002067 K562 cell line Homo sapiens MAX-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF280XEL, ENCFF609KEQ, ENCFF922CBN 1024235 ENCODE Processing Pipeline 747de7bd157b52cb8b23dbf18917e54a https://www.encodeproject.org/files/ENCFF422NGZ/@@download/ENCFF422NGZ.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, control low read depth, low read depth biological replicates with identical biosample ENCFF002CSA bed narrowPeak optimal idr thresholded peaks ENCSR000EDA ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens CEBPB-human DNA see document see document False 2011-10-29 ENCODE 1284848 ENCODE Consortium Analysis Working Group f85716cb7fe3fda2d73d895e930e47c2 https://www.encodeproject.org/files/ENCFF002CSA/@@download/ENCFF002CSA.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF884JKW bed narrowPeak optimal idr thresholded peaks ENCSR000BLF ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens HNF4A-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF167THE, ENCFF176XYE, ENCFF277KXQ 382258 ENCODE Processing Pipeline b34f82ba92cb34b320e67f0328816c72 https://www.encodeproject.org/files/ENCFF884JKW/@@download/ENCFF884JKW.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF002CTB bed narrowPeak optimal idr thresholded peaks ENCSR000EDE ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens RAD21-human DNA see document see document False 2011-10-29 ENCODE 946544 ENCODE Consortium Analysis Working Group 11cdf5ce154b89532bb688f47985f9e2 https://www.encodeproject.org/files/ENCFF002CTB/@@download/ENCFF002CTB.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF634AYU bed narrowPeak optimal idr thresholded peaks ENCSR000FAZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon alpha 30.0 minute MYC-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF517GFP, ENCFF726YHM, ENCFF761YWV 156795 ENCODE Processing Pipeline 730d1f4239612dda93845a2c03f5db0d https://www.encodeproject.org/files/ENCFF634AYU/@@download/ENCFF634AYU.bed.gz hg19 released control low read depth, borderline replicate concordance biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF192BTP bed narrowPeak optimal idr thresholded peaks ENCSR000EZW ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 6.0 hour JUN-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF052OWI, ENCFF394RSM, ENCFF436KCV 111175 ENCODE Processing Pipeline f6d9722fc246ece97dc02a364d78a156 https://www.encodeproject.org/files/ENCFF192BTP/@@download/ENCFF192BTP.bed.gz hg19 released control low read depth, borderline replicate concordance, mixed read lengths biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF395BZZ bed narrowPeak optimal idr thresholded peaks ENCSR000BGA ChIP-seq EFO:0005234 PFSK-1 cell line Homo sapiens FOXP2-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF229DJA, ENCFF882KTD, ENCFF943NWC 302567 ENCODE Processing Pipeline 4e19b95df0695a93ba3dc403d0d64995 https://www.encodeproject.org/files/ENCFF395BZZ/@@download/ENCFF395BZZ.bed.gz hg19 released control low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth extremely low read depth, extremely low read length ENCFF165AUR bed narrowPeak optimal idr thresholded peaks ENCSR000BRL ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour SIX5-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF026LZC, ENCFF838ZHL, ENCFF974EOM 148829 ENCODE Processing Pipeline dcc0af113feb3c7e0cd87e3e67db6c1c https://www.encodeproject.org/files/ENCFF165AUR/@@download/ENCFF165AUR.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF067QUU bed narrowPeak optimal idr thresholded peaks ENCSR000BJH ChIP-seq EFO:0002785 GM12891 cell line Homo sapiens PAX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF385UJM, ENCFF493TPH, ENCFF801IRZ 113118 ENCODE Processing Pipeline 5dad41b367e9fb1f040fcd4a384e1dd0 https://www.encodeproject.org/files/ENCFF067QUU/@@download/ENCFF067QUU.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking ENCFF414FWV bed narrowPeak optimal idr thresholded peaks ENCSR000DWH ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF051RIN, ENCFF095BZW, ENCFF645FWE 998849 ENCODE Processing Pipeline d10b4180a11b1153c93ac953d9ea5b6e https://www.encodeproject.org/files/ENCFF414FWV/@@download/ENCFF414FWV.bed.gz hg19 released low read length, low read depth ENCFF296XCF bed narrowPeak optimal idr thresholded peaks ENCSR000BQE ChIP-seq EFO:0005718 Ishikawa cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour CTCF-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF305MUT, ENCFF542MFI, ENCFF598COF 383004 ENCODE Processing Pipeline c426eb3fba59c258c551f1b9197e8079 https://www.encodeproject.org/files/ENCFF296XCF/@@download/ENCFF296XCF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF498DOQ bed narrowPeak optimal idr thresholded peaks ENCSR000EHK ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 30.0 minute STAT1-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF585NXD, ENCFF763YXP, ENCFF956SIV 18040 ENCODE Processing Pipeline cabac0bdd4bc42dfea03b1f763d569c8 https://www.encodeproject.org/files/ENCFF498DOQ/@@download/ENCFF498DOQ.bed.gz hg19 released mixed read lengths biological replicates with identical biosample control insufficient read depth, insufficient read depth, insufficient replicate concordance, insufficient read length ENCFF654YPN bed narrowPeak optimal idr thresholded peaks ENCSR584GHV ChIP-seq EFO:0001086 A549 cell line Homo sapiens NFE2L2-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF314DTI, ENCFF332PXJ, ENCFF767PWR 137730 ENCODE Processing Pipeline a6c4c723a4a6672ad59f6ac26c2b0c25 https://www.encodeproject.org/files/ENCFF654YPN/@@download/ENCFF654YPN.bed.gz hg19 released low read length, borderline replicate concordance ENCFF760AQQ bed narrowPeak optimal idr thresholded peaks ENCSR000EBZ ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens JUND-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF065SXF, ENCFF162PXN, ENCFF338SNH 233544 ENCODE Processing Pipeline 66b5655b705d61f43eef9a3327e5df2b https://www.encodeproject.org/files/ENCFF760AQQ/@@download/ENCFF760AQQ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF417QAJ bed narrowPeak optimal idr thresholded peaks ENCSR000EZT ChIP-seq EFO:0002067 K562 cell line Homo sapiens interferon gamma 30.0 minute JUN-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF076VIZ, ENCFF646NDI, ENCFF711IWR 149199 ENCODE Processing Pipeline 238b9e00469f275659c398777dc0f553 https://www.encodeproject.org/files/ENCFF417QAJ/@@download/ENCFF417QAJ.bed.gz hg19 released mild to moderate bottlenecking, mixed read lengths biological replicates with identical biosample control insufficient read depth, insufficient read depth, insufficient read length ENCFF453HPD bed narrowPeak optimal idr thresholded peaks ENCSR000BHM ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF116MTZ, ENCFF719OMW, ENCFF935KIG 278409 ENCODE Processing Pipeline 07f8d6d12ffe4b5d81a0bfda84ea298d https://www.encodeproject.org/files/ENCFF453HPD/@@download/ENCFF453HPD.bed.gz hg19 released low read length, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF721HUX bed narrowPeak optimal idr thresholded peaks ENCSR000BGK ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens JUND-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF265CMT, ENCFF323HOG, ENCFF953YCY 480792 ENCODE Processing Pipeline 52a019c14919da9374985ab812f42e9d https://www.encodeproject.org/files/ENCFF721HUX/@@download/ENCFF721HUX.bed.gz hg19 released control low read depth, low read length, low read depth, borderline replicate concordance biological replicates with identical biosample missing control alignments ENCFF543VGD bed narrowPeak optimal idr thresholded peaks ENCSR000DYD ChIP-seq EFO:0001086 A549 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF144GCK, ENCFF320LNM, ENCFF377UTP 783720 ENCODE Processing Pipeline 5ec46ebb8b1b8b0b3efca5ee107976ef https://www.encodeproject.org/files/ENCFF543VGD/@@download/ENCFF543VGD.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment biological replicates with identical biosample ENCFF209MQX bed narrowPeak optimal idr thresholded peaks ENCSR000BRK ChIP-seq EFO:0002067 K562 cell line Homo sapiens TEAD4-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF318EUW, ENCFF740XZM, ENCFF835OES 592931 ENCODE Processing Pipeline 445f3e8cab3b8f9e3271a2b0583cf90c https://www.encodeproject.org/files/ENCFF209MQX/@@download/ENCFF209MQX.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample ENCFF678JII bed narrowPeak optimal idr thresholded peaks ENCSR000ARD ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF178CPV, ENCFF411KUR, ENCFF859FLD 37189 ENCODE Processing Pipeline e89a61b52a33a3db505994d17393df9a https://www.encodeproject.org/files/ENCFF678JII/@@download/ENCFF678JII.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms control insufficient read depth, insufficient read depth ENCFF805GKD bed narrowPeak optimal idr thresholded peaks ENCSR000BGI ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens USF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF083HDR, ENCFF238JYT, ENCFF518BAN 139678 ENCODE Processing Pipeline f645df6ebe696a996c18451fce189d75 https://www.encodeproject.org/files/ENCFF805GKD/@@download/ENCFF805GKD.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, low read depth, mixed read lengths biological replicates with identical biosample insufficient read depth extremely low read length ENCFF629BFI bed narrowPeak optimal idr thresholded peaks ENCSR000EFS ChIP-seq EFO:0002067 K562 cell line Homo sapiens JUN-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF182AWR, ENCFF422SBX, ENCFF596KVH 388538 ENCODE Processing Pipeline 5ebab0cfbc3b0ee3b78931c4d1edd480 https://www.encodeproject.org/files/ENCFF629BFI/@@download/ENCFF629BFI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF195CYT bed narrowPeak optimal idr thresholded peaks ENCSR000EFJ ChIP-seq EFO:0001196 IMR-90 cell line Homo sapiens RAD21-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF058CVP, ENCFF263ADC, ENCFF731ASC 701358 ENCODE Processing Pipeline 4d3907a2d16dc9294acca25831c73b27 https://www.encodeproject.org/files/ENCFF195CYT/@@download/ENCFF195CYT.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CSL bed narrowPeak optimal idr thresholded peaks ENCSR000ECZ ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens GTF2F1-human DNA see document see document False 2011-10-29 ENCODE 302946 ENCODE Consortium Analysis Working Group 6bb4c8493a3be44ede2ce45814c7c621 https://www.encodeproject.org/files/ENCFF002CSL/@@download/ENCFF002CSL.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample, missing derived_from ENCFF002CHQ bed narrowPeak optimal idr thresholded peaks ENCSR000BGQ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SPI1-human DNA see document see document False 2011-07-18 ENCODE 898654 ENCODE Consortium Analysis Working Group 7bfcaceb2634fd60e68d9c6730a55f7b https://www.encodeproject.org/files/ENCFF002CHQ/@@download/ENCFF002CHQ.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from, missing raw data in replicate ENCFF328FUO bed narrowPeak optimal idr thresholded peaks ENCSR000DTW ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF035ZLA, ENCFF326OIK, ENCFF425BCQ 861513 ENCODE Processing Pipeline 46f300b41d4198e9056638c44cfce2fe https://www.encodeproject.org/files/ENCFF328FUO/@@download/ENCFF328FUO.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth extremely low read depth ENCFF938IOJ bed narrowPeak optimal idr thresholded peaks ENCSR000EFW ChIP-seq EFO:0002067 K562 cell line Homo sapiens UBTF-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF377VMB, ENCFF696JUU, ENCFF976ZTX 180556 ENCODE Processing Pipeline c9635f75ccfec61b8087434efc5ee93c https://www.encodeproject.org/files/ENCFF938IOJ/@@download/ENCFF938IOJ.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF544NRC bed narrowPeak optimal idr thresholded peaks ENCSR000BGS ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF270KWZ, ENCFF466MWY, ENCFF626GCR 288644 ENCODE Processing Pipeline c83c2b45f1ee4fc7ad3a0bce44c11279 https://www.encodeproject.org/files/ENCFF544NRC/@@download/ENCFF544NRC.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF917COW bed narrowPeak optimal idr thresholded peaks ENCSR000BLI ChIP-seq EFO:0002067 K562 cell line Homo sapiens E2F6-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF072IAO, ENCFF318UXE, ENCFF373HDQ 534776 ENCODE Processing Pipeline 50091b97c0b4ff0828db52d7241d577e https://www.encodeproject.org/files/ENCFF917COW/@@download/ENCFF917COW.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, control low read depth, low read depth biological replicates with identical biosample insufficient read depth, poor library complexity, severe bottlenecking ENCFF527RGJ bed narrowPeak optimal idr thresholded peaks ENCSR000BLX ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens all-trans-retinoic acid 6 μM 48 hour CTCF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF379KOF, ENCFF520BPM, ENCFF820XSG 663450 ENCODE Processing Pipeline c73c3ed0d619a8a3d5cb1f076dba5ad8 https://www.encodeproject.org/files/ENCFF527RGJ/@@download/ENCFF527RGJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth missing control alignments ENCFF926FUM bed narrowPeak optimal idr thresholded peaks ENCSR000BKU ChIP-seq EFO:0002067 K562 cell line Homo sapiens YY1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF475ICG, ENCFF608RBZ, ENCFF897DAT 268837 ENCODE Processing Pipeline 73708b5a1b2700584fc477fdee757ee3 https://www.encodeproject.org/files/ENCFF926FUM/@@download/ENCFF926FUM.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample control insufficient read depth, insufficient read depth, insufficient replicate concordance extremely low read depth ENCFF963TZI bed narrowPeak optimal idr thresholded peaks ENCSR000BLU ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens TAF7-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF120OKL, ENCFF299QBC, ENCFF435PQI 256893 ENCODE Processing Pipeline 3fbc18f78ff0a967465e5f4f920095e7 https://www.encodeproject.org/files/ENCFF963TZI/@@download/ENCFF963TZI.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF334FMW bed narrowPeak optimal idr thresholded peaks ENCSR000BKT ChIP-seq EFO:0002067 K562 cell line Homo sapiens USF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF278MWT, ENCFF385JVK, ENCFF738UPC 343702 ENCODE Processing Pipeline c8c6a2b189f45df818d83179943cc412 https://www.encodeproject.org/files/ENCFF334FMW/@@download/ENCFF334FMW.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample control insufficient read depth, poor library complexity, severe bottlenecking extremely low read depth ENCFF002CZJ bed narrowPeak optimal idr thresholded peaks ENCSR000EWV ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GATA3-human DNA see document see document False 2011-10-29 ENCODE 161667 ENCODE Consortium Analysis Working Group eef7fcc9c11b39e4bcfe336e069c07cd https://www.encodeproject.org/files/ENCFF002CZJ/@@download/ENCFF002CZJ.bed.gz hg19 released low read length, inconsistent platforms missing derived_from, biological replicates with identical biosample ENCFF812QPN bed narrowPeak optimal idr thresholded peaks ENCSR000EGX ChIP-seq EFO:0002067 K562 cell line Homo sapiens MAFK-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF072BMK, ENCFF660EKS, ENCFF887IBL 482148 ENCODE Processing Pipeline 9508b48c5610d3882fe8c0e0e9bbd23e https://www.encodeproject.org/files/ENCFF812QPN/@@download/ENCFF812QPN.bed.gz hg19 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF885KLR bed narrowPeak optimal idr thresholded peaks ENCSR663WAR ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens REST-human DNA False 2017-01-08 ENCODE 1, 2 ENCFF001TDO, ENCFF029AGK, ENCFF371JLL, ENCFF651ZPC 115171 ENCODE Processing Pipeline f20eefcfc1e4a4ed95f2d2d253a7750b https://www.encodeproject.org/files/ENCFF885KLR/@@download/ENCFF885KLR.bed.gz hg19 released low read length, low read depth, antibody characterized with exemption, mixed read lengths ENCFF564WEB bed narrowPeak optimal idr thresholded peaks ENCSR000BMD ChIP-seq EFO:0002067 K562 cell line Homo sapiens ELF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF445HQE, ENCFF634DSI, ENCFF875HXY 561894 ENCODE Processing Pipeline eacf14da9a574f49fd8a632a87be3b4d https://www.encodeproject.org/files/ENCFF564WEB/@@download/ENCFF564WEB.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample poor library complexity, insufficient replicate concordance, severe bottlenecking extremely low read depth ENCFF002CHV bed narrowPeak optimal idr thresholded peaks ENCSR000BHK ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens SP1-human DNA see document see document False 2011-07-18 ENCODE 357355 ENCODE Consortium Analysis Working Group f3352a8a478ebcbe54fda2f2becbd4eb https://www.encodeproject.org/files/ENCFF002CHV/@@download/ENCFF002CHV.bed.gz hg19 released low read length missing derived_from, missing raw data in replicate ENCFF450CNK bed narrowPeak optimal idr thresholded peaks ENCSR203QEB ChIP-seq EFO:0002713 Panc1 cell line Homo sapiens CTCF-human DNA False 2017-07-21 ENCODE 1, 2 ENCFF001TDO, ENCFF032KSH, ENCFF255EDE, ENCFF563CXH 1438655 ENCODE Processing Pipeline 2c3f3e32ca1959fa2952b084fb115bed https://www.encodeproject.org/files/ENCFF450CNK/@@download/ENCFF450CNK.bed.gz hg19 released mild to moderate bottlenecking NTR biosample ENCFF898MUV bed narrowPeak optimal idr thresholded peaks ENCSR000DZC ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens RCOR1-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF118LBD, ENCFF489ZRF, ENCFF906FFH 197171 ENCODE Processing Pipeline 590976200dc7a4de06cc75f4f0991b60 https://www.encodeproject.org/files/ENCFF898MUV/@@download/ENCFF898MUV.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF380TJK bed narrowPeak optimal idr thresholded peaks ENCSR000ARH ChIP-seq CL:0000515 skeletal muscle myoblast primary cell Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF442AZU, ENCFF801WBW, ENCFF965BIL 40740 ENCODE Processing Pipeline fd7bd8fb764b03f70431855e8c0e1d12 https://www.encodeproject.org/files/ENCFF380TJK/@@download/ENCFF380TJK.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF371OGO bed narrowPeak optimal idr thresholded peaks ENCSR000DYP ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens ZNF384-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF745TRP, ENCFF824VGN, ENCFF967EHX 253028 ENCODE Processing Pipeline d302851e104dd8ae0a5b6a49c01de18c https://www.encodeproject.org/files/ENCFF371OGO/@@download/ENCFF371OGO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CVW bed narrowPeak optimal idr thresholded peaks ENCSR000FAI ChIP-seq EFO:0002067 K562 cell line Homo sapiens FOS-human DNA see document see document False 2011-10-29 ENCODE 153814 ENCODE Consortium Analysis Working Group 6dcfdb373210f92a6f160dc9869db949 https://www.encodeproject.org/files/ENCFF002CVW/@@download/ENCFF002CVW.bed.gz hg19 released duplicate lane review, biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CXU bed narrowPeak optimal idr thresholded peaks ENCSR000FAD ChIP-seq EFO:0002067 K562 cell line Homo sapiens RAD21-human DNA see document see document False 2011-10-29 ENCODE 367853 ENCODE Consortium Analysis Working Group 37b2c03ce75692dc617fa321d3f65c51 https://www.encodeproject.org/files/ENCFF002CXU/@@download/ENCFF002CXU.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF445ATY bed narrowPeak optimal idr thresholded peaks ENCSR000DLB ChIP-seq EFO:0005346 GM13977 cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF336VRJ, ENCFF637DKG, ENCFF807PRZ 750841 ENCODE Processing Pipeline 9cb6f944b978f18fb4831d56fa835b97 https://www.encodeproject.org/files/ENCFF445ATY/@@download/ENCFF445ATY.bed.gz hg19 released control low read depth, mild to moderate bottlenecking, low read depth biological replicates with identical biosample insufficient read depth missing control alignments ENCFF156CFD bed narrowPeak optimal idr thresholded peaks ENCSR000ASE ChIP-seq CL:0002551 fibroblast of dermis primary cell Homo sapiens EZH2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF226DWG, ENCFF551TJN, ENCFF585OAO 236848 ENCODE Processing Pipeline be0dd461421f8d0c3111eab20915f28c https://www.encodeproject.org/files/ENCFF156CFD/@@download/ENCFF156CFD.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth ENCFF861DPF bed narrowPeak optimal idr thresholded peaks ENCSR000EIC ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens CTCF-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF079HZU, ENCFF781THQ, ENCFF960NKG 888678 ENCODE Processing Pipeline 2669e0f55968e04ed42440428a06c9df https://www.encodeproject.org/files/ENCFF861DPF/@@download/ENCFF861DPF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF526NYA bed narrowPeak optimal idr thresholded peaks ENCSR000BIJ ChIP-seq EFO:0002785 GM12891 cell line Homo sapiens SPI1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF200SPQ, ENCFF427TMP, ENCFF461JCM 921797 ENCODE Processing Pipeline 3849889c70e956a9bcfb72dea5ee2b35 https://www.encodeproject.org/files/ENCFF526NYA/@@download/ENCFF526NYA.bed.gz hg19 released control low read depth, low read length, low read depth biological replicates with identical biosample ENCFF854KPC bed narrowPeak optimal idr thresholded peaks ENCSR000BOT ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens REST-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF172OLJ, ENCFF543QRY, ENCFF658GRO 286172 ENCODE Processing Pipeline d364c2fca920aaecc8c604ba03c2b902 https://www.encodeproject.org/files/ENCFF854KPC/@@download/ENCFF854KPC.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF002CZM bed narrowPeak optimal idr thresholded peaks ENCSR000EWT ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens TCF7L2-human DNA see document see document False 2011-10-29 ENCODE 263955 ENCODE Consortium Analysis Working Group 79a1ee48bf1fd09b432fe6f730783b9d https://www.encodeproject.org/files/ENCFF002CZM/@@download/ENCFF002CZM.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample, missing derived_from ENCFF888JDR bed narrowPeak optimal idr thresholded peaks ENCSR843ZUP ChIP-seq CL:0002319 neural cell in vitro differentiated cells Homo sapiens EP300-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF114UVX, ENCFF287VNA, ENCFF777EIJ 829546 ENCODE Processing Pipeline c2b6e7c7a961f98ca60edd5977ebb6dc https://www.encodeproject.org/files/ENCFF888JDR/@@download/ENCFF888JDR.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF034CQR bed narrowPeak optimal idr thresholded peaks ENCSR000BNM ChIP-seq EFO:0002067 K562 cell line Homo sapiens TAF7-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF070BNL, ENCFF271GZS, ENCFF611EGN 11755 ENCODE Processing Pipeline 7a373886ebf5e3085fc3dd43d0d662da https://www.encodeproject.org/files/ENCFF034CQR/@@download/ENCFF034CQR.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample control insufficient read depth ENCFF638OUB bed narrowPeak optimal idr thresholded peaks ENCSR000APM ChIP-seq CL:0002551 fibroblast of dermis primary cell Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF180UME, ENCFF326AWX, ENCFF622MTR 769456 ENCODE Processing Pipeline d417f489c6a7b0ca45096009a20f040e https://www.encodeproject.org/files/ENCFF638OUB/@@download/ENCFF638OUB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity NTR biosample insufficient read depth, severe bottlenecking missing control alignments ENCFF751GGI bed narrowPeak optimal idr thresholded peaks ENCSR000ATC ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens EZH2-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF233VOB, ENCFF427OVX, ENCFF981RBQ 57412 ENCODE Processing Pipeline 7aedab00b9f60d6da4433352c11c9015 https://www.encodeproject.org/files/ENCFF751GGI/@@download/ENCFF751GGI.bed.gz hg19 released low read length, mild to moderate bottlenecking, inconsistent platforms ENCFF002CSX bed narrowPeak optimal idr thresholded peaks ENCSR000ECV ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens EP300-human DNA see document see document False 2011-10-29 ENCODE 609315 ENCODE Consortium Analysis Working Group 11543569f44a558a29a45baff1a62ddf https://www.encodeproject.org/files/ENCFF002CSX/@@download/ENCFF002CSX.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF220YOA bed narrowPeak optimal idr thresholded peaks ENCSR000EYB ChIP-seq EFO:0002717 SH-SY5Y cell line Homo sapiens GATA2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF086NRZ, ENCFF325FPK, ENCFF770MLZ 588315 ENCODE Processing Pipeline 79a450617ab593291997e806ddec83f4 https://www.encodeproject.org/files/ENCFF220YOA/@@download/ENCFF220YOA.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF002CTE bed narrowPeak optimal idr thresholded peaks ENCSR000ECS ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens SMC3-human DNA see document see document False 2011-10-29 ENCODE 939484 ENCODE Consortium Analysis Working Group 4fbd9b20cc5b419c3086e3ca689fe9ee https://www.encodeproject.org/files/ENCFF002CTE/@@download/ENCFF002CTE.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF468CFJ bed narrowPeak optimal idr thresholded peaks ENCSR000AVB ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens HDAC2-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF327ORV, ENCFF756FVQ, ENCFF848MDV 335244 ENCODE Processing Pipeline 88657f3ff9fbb5c3e01288866fcfba99 https://www.encodeproject.org/files/ENCFF468CFJ/@@download/ENCFF468CFJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity ENCFF002CZP bed narrowPeak optimal idr thresholded peaks ENCSR000EHS ChIP-seq EFO:0002798 NB4 cell line Homo sapiens MAX-human DNA see document see document False 2011-10-29 ENCODE 796018 ENCODE Consortium Analysis Working Group 5f98fed6e18417827c6df77859c1cf0e https://www.encodeproject.org/files/ENCFF002CZP/@@download/ENCFF002CZP.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF402JJK bed narrowPeak optimal idr thresholded peaks ENCSR000BNH ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens CTCF-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF289JUZ, ENCFF722MDG, ENCFF775VDO 888822 ENCODE Processing Pipeline f1680aa6ab0504910c3a639cd354bd47 https://www.encodeproject.org/files/ENCFF402JJK/@@download/ENCFF402JJK.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms, moderate library complexity biological replicates with identical biosample missing control alignments ENCFF182QDI bed narrowPeak optimal idr thresholded peaks ENCSR000BNE ChIP-seq EFO:0002067 K562 cell line Homo sapiens EGR1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF511ZEU, ENCFF537QVM, ENCFF671MRQ 630223 ENCODE Processing Pipeline 32b8aef967771ff7865454fc10cc9ab3 https://www.encodeproject.org/files/ENCFF182QDI/@@download/ENCFF182QDI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample control insufficient read depth ENCFF757CRW bed narrowPeak optimal idr thresholded peaks ENCSR000EUI ChIP-seq EFO:0005333 GM08714 cell line Homo sapiens ZNF274-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF238OBY, ENCFF448IAU, ENCFF624BNC 19404 ENCODE Processing Pipeline 1362aba67dcd62317c81e96eb29b58e0 https://www.encodeproject.org/files/ENCFF757CRW/@@download/ENCFF757CRW.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF002DAI bed narrowPeak optimal idr thresholded peaks ENCSR000DKU ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MYC-human DNA see document see document False 2011-03-17 ENCODE 89590 ENCODE Consortium Analysis Working Group 6520b2bab2bb01aa3703ef80e352b4c0 https://www.encodeproject.org/files/ENCFF002DAI/@@download/ENCFF002DAI.bed.gz hg19 released low read length, inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF609ETO bed narrowPeak optimal idr thresholded peaks ENCSR000APF ChIP-seq CL:0000062 osteoblast primary cell Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF339XPB, ENCFF397OQE, ENCFF757USJ 771426 ENCODE Processing Pipeline f18afe6d9ac8129dd7c728a8434763f5 https://www.encodeproject.org/files/ENCFF609ETO/@@download/ENCFF609ETO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity NTR biosample extremely low read depth ENCFF694SEF bed narrowPeak optimal idr thresholded peaks ENCSR000DMH ChIP-seq UBERON:0002048 lung tissue Homo sapiens CTCF-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF202BTH, ENCFF306ACX, ENCFF553SJU 349464 ENCODE Processing Pipeline b1dde7461d8305cdcaa652804ba6b72d https://www.encodeproject.org/files/ENCFF694SEF/@@download/ENCFF694SEF.bed.gz hg19 released mild to moderate bottlenecking control extremely low read depth, extremely low read depth ENCFF176YNV bed narrowPeak optimal idr thresholded peaks ENCSR000DMR ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF574PXY, ENCFF853XFI, ENCFF993IKO 1333405 ENCODE Processing Pipeline 0b315f031f7a61a307a180b6362a29bf https://www.encodeproject.org/files/ENCFF176YNV/@@download/ENCFF176YNV.bed.gz hg19 released low read length, mild to moderate bottlenecking biological replicates with identical biosample ENCFF695IQU bed narrowPeak optimal idr thresholded peaks ENCSR000DMQ ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MYC-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF153LKX, ENCFF787DCF, ENCFF819JEC 568613 ENCODE Processing Pipeline f9b5662aa7654ed4987bf58839091041 https://www.encodeproject.org/files/ENCFF695IQU/@@download/ENCFF695IQU.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF002CSV bed narrowPeak optimal idr thresholded peaks ENCSR000DNR ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens NFYB-human DNA see document see document False 2011-10-29 ENCODE 176124 ENCODE Consortium Analysis Working Group 25d644731439a2bfeab2c0fd6d75a7ff https://www.encodeproject.org/files/ENCFF002CSV/@@download/ENCFF002CSV.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF841IFL bed narrowPeak optimal idr thresholded peaks ENCSR000BHE ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 500 pM 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF277VVP, ENCFF660YDK, ENCFF875UKZ 37448 ENCODE Processing Pipeline 99a7cd47d14f820001e3c8498baebe7d https://www.encodeproject.org/files/ENCFF841IFL/@@download/ENCFF841IFL.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CTO bed narrowPeak optimal idr thresholded peaks ENCSR000ECJ ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZKSCAN1-human DNA see document see document False 2012-05-14 ENCODE 108760 ENCODE Consortium Analysis Working Group 5599b7953ea928f46244fadce1a07df5 https://www.encodeproject.org/files/ENCFF002CTO/@@download/ENCFF002CTO.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF002CQB bed narrowPeak optimal idr thresholded peaks ENCSR000EAN ChIP-seq EFO:0002786 GM12892 cell line Homo sapiens tumor necrosis factor 25 ng/mL 6 hour RELA-human DNA see document see document False 2011-10-29 ENCODE 197610 ENCODE Consortium Analysis Working Group a521d8594d1306ceb49e88c81a07b044 https://www.encodeproject.org/files/ENCFF002CQB/@@download/ENCFF002CQB.bed.gz hg19 released missing derived_from, biological replicates with identical biosample insufficient read length ENCFF255EOB bed narrowPeak optimal idr thresholded peaks ENCSR000BRS ChIP-seq EFO:0002067 K562 cell line Homo sapiens NR2F2-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF622IDZ, ENCFF829WNA, ENCFF952DON 359095 ENCODE Processing Pipeline 261091a7cd8dcdf58adf98e3c6d32d2b https://www.encodeproject.org/files/ENCFF255EOB/@@download/ENCFF255EOB.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms biological replicates with identical biosample ENCFF065LHJ bed narrowPeak optimal idr thresholded peaks ENCSR000DTA ChIP-seq CL:2000044 brain microvascular endothelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF113ITH, ENCFF163DTZ, ENCFF222LZR 978732 ENCODE Processing Pipeline 75759957f5c6749d741f15b5790add81 https://www.encodeproject.org/files/ENCFF065LHJ/@@download/ENCFF065LHJ.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth missing control alignments ENCFF308IXJ bed narrowPeak optimal idr thresholded peaks ENCSR000EGI ChIP-seq EFO:0002067 K562 cell line Homo sapiens MAFF-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF583NBG, ENCFF755LJZ, ENCFF864KPF 460910 ENCODE Processing Pipeline 681c4962a27c4e34b59fc8490e917288 https://www.encodeproject.org/files/ENCFF308IXJ/@@download/ENCFF308IXJ.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF470PNM bed narrowPeak optimal idr thresholded peaks ENCSR000DXD ChIP-seq CL:0002306 epithelial cell of proximal tubule primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF077RDH, ENCFF447AUB, ENCFF943ZQC 985515 ENCODE Processing Pipeline a32833a04672558d1873a39e47f77f68 https://www.encodeproject.org/files/ENCFF470PNM/@@download/ENCFF470PNM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth ENCFF682AWN bed narrowPeak optimal idr thresholded peaks ENCSR000DMM ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens MYC-human DNA see document see document False 2012-08-27 ENCODE 1, 2 ENCFF001TDO, ENCFF434LJJ, ENCFF673PRZ, ENCFF844RNW 489114 ENCODE Processing Pipeline 2e5f5e8319184cefc7e36f4668843e09 https://www.encodeproject.org/files/ENCFF682AWN/@@download/ENCFF682AWN.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample poor library complexity ENCFF732XGR bed narrowPeak optimal idr thresholded peaks ENCSR000ECE ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens RAD21-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF190MWS, ENCFF656HTA, ENCFF680SHJ 1032500 ENCODE Processing Pipeline 31956512aead9d11c3421ce3768da5a2 https://www.encodeproject.org/files/ENCFF732XGR/@@download/ENCFF732XGR.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002DBF bed narrowPeak optimal idr thresholded peaks ENCSR000DMP ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens 17β-estradiol 100 nM 45 minute MYC-human DNA see document see document False 2011-03-17 ENCODE 261259 ENCODE Consortium Analysis Working Group a4163c1c19e13c3d6733f2b633a77109 https://www.encodeproject.org/files/ENCFF002DBF/@@download/ENCFF002DBF.bed.gz hg19 released low read length, mild to moderate bottlenecking missing derived_from, biological replicates with identical biosample ENCFF002DBM bed narrowPeak optimal idr thresholded peaks ENCSR000DMV ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1209029 ENCODE Consortium Analysis Working Group 160ceb49b8fe9537a5bbe91df7dd428a https://www.encodeproject.org/files/ENCFF002DBM/@@download/ENCFF002DBM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample, missing derived_from ENCFF374FKH bed narrowPeak optimal idr thresholded peaks ENCSR000DOT ChIP-seq EFO:0001200 MCF 10A cell line Homo sapiens ethanol 0.01 percent 36.0 hour FOS-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF099KUG, ENCFF581HNC, ENCFF658PKF 1202193 ENCODE Processing Pipeline c4ab2acaa7200fb9186d11f8cd36679d https://www.encodeproject.org/files/ENCFF374FKH/@@download/ENCFF374FKH.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, missing genetic modification characterization duplicate lane review, biological replicates with identical biosample ENCFF002CZN bed narrowPeak optimal idr thresholded peaks ENCSR000EWU ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens ZNF217-human DNA see document see document False 2011-10-29 ENCODE 258184 ENCODE Consortium Analysis Working Group 3bb1a2b50508c062084f4916f14d2b83 https://www.encodeproject.org/files/ENCFF002CZN/@@download/ENCFF002CZN.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF345GZF bed narrowPeak optimal idr thresholded peaks ENCSR000BJN ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens TAF1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF243XCD, ENCFF602IZZ, ENCFF999FLX 299587 ENCODE Processing Pipeline 832d28b82a0ce751fca92ccb2b2b795e https://www.encodeproject.org/files/ENCFF345GZF/@@download/ENCFF345GZF.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF558VPP bed narrowPeak optimal idr thresholded peaks ENCSR000BMW ChIP-seq EFO:0002067 K562 cell line Homo sapiens REST-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF051ITR, ENCFF621KLV, ENCFF764CZH 239761 ENCODE Processing Pipeline 810c09de8b3c3fe318e8643e8c5b7e2a https://www.encodeproject.org/files/ENCFF558VPP/@@download/ENCFF558VPP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample control insufficient read depth, insufficient read depth, poor library complexity, severe bottlenecking ENCFF288RFS bed narrowPeak optimal idr thresholded peaks ENCSR000DUS ChIP-seq CL:0002327 mammary epithelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF924YJI, ENCFF929WKT, ENCFF938HQH 889632 ENCODE Processing Pipeline 7ce3d71abd0220f4289d7b0aced11dc4 https://www.encodeproject.org/files/ENCFF288RFS/@@download/ENCFF288RFS.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF033EBX bed narrowPeak optimal idr thresholded peaks ENCSR000BNW ChIP-seq EFO:0002067 K562 cell line Homo sapiens SIX5-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF066ONU, ENCFF521MOS, ENCFF738BIG 62476 ENCODE Processing Pipeline 097bf841440b7b7f1ef9cb01097fd511 https://www.encodeproject.org/files/ENCFF033EBX/@@download/ENCFF033EBX.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF002CSF bed narrowPeak optimal idr thresholded peaks ENCSR000ECM ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens RCOR1-human DNA see document see document False 2012-05-14 ENCODE 394882 ENCODE Consortium Analysis Working Group e7c99d8ef0836c01ae22ce43c8fbe510 https://www.encodeproject.org/files/ENCFF002CSF/@@download/ENCFF002CSF.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF833FTF bed narrowPeak optimal idr thresholded peaks ENCSR000AKB ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF551KNM, ENCFF706QLS, ENCFF934NEI 655789 ENCODE Processing Pipeline 265cfe705263baae508111a4114aab61 https://www.encodeproject.org/files/ENCFF833FTF/@@download/ENCFF833FTF.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, low read depth, mixed read lengths control insufficient read depth, insufficient read depth ENCFF002CRW bed narrowPeak optimal idr thresholded peaks ENCSR000EDB ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens BRCA1-human DNA see document see document False 2011-10-29 ENCODE 211374 ENCODE Consortium Analysis Working Group db45e389b7cf2fe24e3b9151c2c27b26 https://www.encodeproject.org/files/ENCFF002CRW/@@download/ENCFF002CRW.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF295AWO bed narrowPeak optimal idr thresholded peaks ENCSR000DRP ChIP-seq EFO:0001160 GM12873 cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 3 ENCFF001TDO, ENCFF247DGH, ENCFF380UJY, ENCFF728WXF 816014 ENCODE Processing Pipeline 5a6de8426a7aa0847344dedf53b3ab41 https://www.encodeproject.org/files/ENCFF295AWO/@@download/ENCFF295AWO.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, moderate library complexity missing raw data in replicate insufficient read depth missing control alignments ENCFF062SBW bed narrowPeak optimal idr thresholded peaks ENCSR000EUQ ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens SUZ12-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF380NLL, ENCFF651DQM, ENCFF940PJA 76539 ENCODE Processing Pipeline 0ceda548faa288b705b6a4c1090317b6 https://www.encodeproject.org/files/ENCFF062SBW/@@download/ENCFF062SBW.bed.gz hg19 released borderline replicate concordance, low read depth biological replicates with identical biosample insufficient read depth, insufficient read length ENCFF002CZO bed narrowPeak optimal idr thresholded peaks ENCSR000EHR ChIP-seq EFO:0002798 NB4 cell line Homo sapiens MYC-human DNA see document see document False 2011-10-29 ENCODE 642994 ENCODE Consortium Analysis Working Group 57ca7f5aea6377a2d1fef98fef2facd7 https://www.encodeproject.org/files/ENCFF002CZO/@@download/ENCFF002CZO.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF492YMU bed narrowPeak optimal idr thresholded peaks ENCSR000BQZ ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens STAT5A-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF447TGK, ENCFF772NOR, ENCFF876BBG 198904 ENCODE Processing Pipeline c5f6d5dee5e25313d5e5dd85604244b8 https://www.encodeproject.org/files/ENCFF492YMU/@@download/ENCFF492YMU.bed.gz hg19 released low read length, inconsistent platforms biological replicates with identical biosample ENCFF882YQH bed narrowPeak optimal idr thresholded peaks ENCSR000DQN ChIP-seq EFO:0001099 Caco-2 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF146XLM, ENCFF450FYB, ENCFF532LQQ 759010 ENCODE Processing Pipeline 7251e79d7216a84cc06fd9967db74d19 https://www.encodeproject.org/files/ENCFF882YQH/@@download/ENCFF882YQH.bed.gz hg19 released moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth insufficient read depth, severe bottlenecking ENCFF413VUC bed narrowPeak optimal idr thresholded peaks ENCSR000BRH ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens MTA3-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF496UYK, ENCFF574RLW, ENCFF600RTA 322940 ENCODE Processing Pipeline 986211e162ebe80002d15d053f4e37f8 https://www.encodeproject.org/files/ENCFF413VUC/@@download/ENCFF413VUC.bed.gz hg19 released low read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF835LPJ bed narrowPeak optimal idr thresholded peaks ENCSR000EXL ChIP-seq EFO:0002713 Panc1 cell line Homo sapiens TCF7L2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF287WRJ, ENCFF349TEE, ENCFF449DID 334695 ENCODE Processing Pipeline fc1aebabccf0ab50b0c6d56b89b23309 https://www.encodeproject.org/files/ENCFF835LPJ/@@download/ENCFF835LPJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, inconsistent platforms biological replicates with identical biosample ENCFF507XOB bed narrowPeak optimal idr thresholded peaks ENCSR000AUC ChIP-seq EFO:0002067 K562 cell line Homo sapiens SUZ12-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF692UFO, ENCFF731WWO, ENCFF809XWY 55253 ENCODE Processing Pipeline cb67e6e280eb53c71e244ba182a543c1 https://www.encodeproject.org/files/ENCFF507XOB/@@download/ENCFF507XOB.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, mixed read lengths missing raw data in replicate insufficient read depth, poor library complexity, insufficient replicate concordance, severe bottlenecking ENCFF002CTP bed narrowPeak optimal idr thresholded peaks ENCSR000ECO ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens ZNF143-human DNA see document see document False 2011-10-29 ENCODE 181234 ENCODE Consortium Analysis Working Group 5dad024c53e1b5eac7fb473933432908 https://www.encodeproject.org/files/ENCFF002CTP/@@download/ENCFF002CTP.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF002CZK bed narrowPeak optimal idr thresholded peaks ENCSR000EWS ChIP-seq EFO:0001203 MCF-7 cell line Homo sapiens GATA3-human DNA see document see document False 2012-05-14 ENCODE 309354 ENCODE Consortium Analysis Working Group f033be2179122e4ba03dac8731653c5b https://www.encodeproject.org/files/ENCFF002CZK/@@download/ENCFF002CZK.bed.gz hg19 released low read length, mixed read lengths missing derived_from, biological replicates with identical biosample insufficient read length ENCFF618DDO bed narrowPeak optimal idr thresholded peaks ENCSR822CEA ChIP-seq CL:0002319 neural cell in vitro differentiated cells Homo sapiens CTCF-human DNA False 2014-07-07 ENCODE 1, 2 ENCFF001TDO, ENCFF496NEE, ENCFF762DPO, ENCFF900WDP 896089 ENCODE Processing Pipeline dd513e682e5bfda211bce2fc3140257c https://www.encodeproject.org/files/ENCFF618DDO/@@download/ENCFF618DDO.bed.gz hg19 released mild to moderate bottlenecking, moderate library complexity, antibody characterized with exemption experiment not submitted to GEO poor library complexity, severe bottlenecking ENCFF076YZO bed narrowPeak optimal idr thresholded peaks ENCSR000BKQ ChIP-seq EFO:0002067 K562 cell line Homo sapiens ETS1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF122POU, ENCFF128BVU, ENCFF927YRG 214196 ENCODE Processing Pipeline 124c1fdf52bdb35192e1849070affed9 https://www.encodeproject.org/files/ENCFF076YZO/@@download/ENCFF076YZO.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample control insufficient read depth ENCFF380FJL bed narrowPeak optimal idr thresholded peaks ENCSR000EHA ChIP-seq EFO:0002067 K562 cell line Homo sapiens TBP-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF523ODF, ENCFF545FAT, ENCFF891AHH 395661 ENCODE Processing Pipeline 119c19af83bd82e64f13fb0805f4b209 https://www.encodeproject.org/files/ENCFF380FJL/@@download/ENCFF380FJL.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF632NQI bed narrowPeak optimal idr thresholded peaks ENCSR000EFT ChIP-seq EFO:0002067 K562 cell line Homo sapiens GATA1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF234GQW, ENCFF253DCO, ENCFF916MQB 261856 ENCODE Processing Pipeline e0454bcca2f35d6ec9a1ad5aca4d6ebc https://www.encodeproject.org/files/ENCFF632NQI/@@download/ENCFF632NQI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, inconsistent target of control experiment biological replicates with identical biosample ENCFF833FCO bed narrowPeak optimal idr thresholded peaks ENCSR000BLO ChIP-seq EFO:0002067 K562 cell line Homo sapiens GABPA-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF276DPB, ENCFF442HXQ, ENCFF961HHN 265021 ENCODE Processing Pipeline c99ce128576687bc8a287943d3473029 https://www.encodeproject.org/files/ENCFF833FCO/@@download/ENCFF833FCO.bed.gz hg19 released low read length, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample control insufficient read depth, insufficient read depth, poor library complexity, severe bottlenecking ENCFF495YRW bed narrowPeak optimal idr thresholded peaks ENCSR000BJT ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF810TPO, ENCFF900AOD, ENCFF918SQN 187680 ENCODE Processing Pipeline da6ed4c9e0e8cd425a6062a294c924dd https://www.encodeproject.org/files/ENCFF495YRW/@@download/ENCFF495YRW.bed.gz hg19 released control low read depth, low read length, low read depth biological replicates with identical biosample insufficient read depth ENCFF671DOL bed narrowPeak optimal idr thresholded peaks ENCSR000EFZ ChIP-seq EFO:0002067 K562 cell line Homo sapiens UBTF-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF507ZLI, ENCFF512HLJ, ENCFF621XGL 356609 ENCODE Processing Pipeline 64dc4d3e4a826b90341dc7f40f98f446 https://www.encodeproject.org/files/ENCFF671DOL/@@download/ENCFF671DOL.bed.gz hg19 released low read length, low read depth, moderate library complexity, inconsistent target of control experiment biological replicates with identical biosample ENCFF448MBM bed narrowPeak optimal idr thresholded peaks ENCSR000ANS ChIP-seq CL:0002372 myotube in vitro differentiated cells Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF004UUL, ENCFF315KYG, ENCFF752POC 727915 ENCODE Processing Pipeline 159eaf588d42788b8035074162a5131a https://www.encodeproject.org/files/ENCFF448MBM/@@download/ENCFF448MBM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity NTR biosample insufficient read depth missing control alignments ENCFF002CTC bed narrowPeak optimal idr thresholded peaks ENCSR000ECX ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens RFX5-human DNA see document see document False 2011-10-29 ENCODE 491540 ENCODE Consortium Analysis Working Group fd13b9cd1c4c3c3b238a627f35349f2f https://www.encodeproject.org/files/ENCFF002CTC/@@download/ENCFF002CTC.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF002CTH bed narrowPeak optimal idr thresholded peaks ENCSR000EDC ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens STAT3-human DNA see document see document False 2011-10-29 ENCODE 348525 ENCODE Consortium Analysis Working Group 9d04aa699bf6a49606986f1798d9d4f8 https://www.encodeproject.org/files/ENCFF002CTH/@@download/ENCFF002CTH.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF002CUA bed narrowPeak optimal idr thresholded peaks ENCSR000EEW ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens forskolin and pyruvate 6.0 hour ESRRA-human DNA see document see document False 2011-10-29 ENCODE 26113 ENCODE Consortium Analysis Working Group 07cbe352ae64551deba3c8aaf9c673ce https://www.encodeproject.org/files/ENCFF002CUA/@@download/ENCFF002CUA.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF179NDS bed narrowPeak optimal idr thresholded peaks ENCSR000EGV ChIP-seq EFO:0002067 K562 cell line Homo sapiens BHLHE40-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF077KRK, ENCFF159GKF, ENCFF368XWG 491465 ENCODE Processing Pipeline 8a7b06a474913c6365c15ef047a6db83 https://www.encodeproject.org/files/ENCFF179NDS/@@download/ENCFF179NDS.bed.gz hg19 released low read length, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF002CSS bed narrowPeak optimal idr thresholded peaks ENCSR000ECL ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MAZ-human DNA see document see document False 2012-05-14 ENCODE 347669 ENCODE Consortium Analysis Working Group 90db788031b3e93cd69f1dcdac0ece8a https://www.encodeproject.org/files/ENCFF002CSS/@@download/ENCFF002CSS.bed.gz hg19 released low read length, inconsistent platforms missing derived_from, biological replicates with identical biosample ENCFF944VAE bed narrowPeak optimal idr thresholded peaks ENCSR000DPF ChIP-seq EFO:0001086 A549 cell line Homo sapiens CTCF-human DNA see document see document False 2012-01-17 ENCODE 1, 2 ENCFF001TDO, ENCFF096GLZ, ENCFF115DAO, ENCFF605UGV 742448 ENCODE Processing Pipeline 27944057da59b906cd704d994fbe20b7 https://www.encodeproject.org/files/ENCFF944VAE/@@download/ENCFF944VAE.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, control low read depth, low read depth poor library complexity, severe bottlenecking extremely low read depth ENCFF002CTJ bed narrowPeak optimal idr thresholded peaks ENCSR000EVF ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens TCF7L2-human DNA see document see document False 2011-10-29 ENCODE 76399 ENCODE Consortium Analysis Working Group 2e76c88be228740a9d90c18ab9105425 https://www.encodeproject.org/files/ENCFF002CTJ/@@download/ENCFF002CTJ.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF598ZLV bed narrowPeak optimal idr thresholded peaks ENCSR000BSK ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens JUND-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF101JCE, ENCFF514HVB, ENCFF866YBG 676842 ENCODE Processing Pipeline 3f6042bd4ab7bb38270b70206d900dd3 https://www.encodeproject.org/files/ENCFF598ZLV/@@download/ENCFF598ZLV.bed.gz hg19 released biological replicates with identical biosample missing control alignments ENCFF657VJX bed narrowPeak optimal idr thresholded peaks ENCSR000AQG ChIP-seq EFO:0002067 K562 cell line Homo sapiens HDAC2-human DNA see document see document False 2012-03-06 ENCODE 1, 2 ENCFF001TDO, ENCFF233XEO, ENCFF680CDC, ENCFF930KIS 93415 ENCODE Processing Pipeline e7464d52ba1f458c1b5e6a0c4a1cfecd https://www.encodeproject.org/files/ENCFF657VJX/@@download/ENCFF657VJX.bed.gz hg19 released borderline replicate concordance, moderate library complexity, low read length, mild to moderate bottlenecking, inconsistent platforms, control low read depth, low read depth ENCFF405BKG bed narrowPeak optimal idr thresholded peaks ENCSR000ECK ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MAFK-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF123SPG, ENCFF742HOV, ENCFF796KTU 323459 ENCODE Processing Pipeline 883649f54d85c599af51713df8eb0cf7 https://www.encodeproject.org/files/ENCFF405BKG/@@download/ENCFF405BKG.bed.gz hg19 released low read length, borderline replicate concordance, low read depth, inconsistent target of control experiment biological replicates with identical biosample, inconsistent mapped reads lengths ENCFF126CZP bed narrowPeak optimal idr thresholded peaks ENCSR000AUZ ChIP-seq CL:0000236 B cell primary cell Homo sapiens EZH2-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF499CWW, ENCFF755RMC, ENCFF814VNW 52060 ENCODE Processing Pipeline 225d1f6f7e7aff79d4fd72818320f140 https://www.encodeproject.org/files/ENCFF126CZP/@@download/ENCFF126CZP.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity poor library complexity, severe bottlenecking extremely low read depth ENCFF587OBC bed narrowPeak optimal idr thresholded peaks ENCSR000BUW ChIP-seq EFO:0002793 HL-60 cell line Homo sapiens SPI1-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF214RQX, ENCFF446FKN, ENCFF670PLH 1034005 ENCODE Processing Pipeline cba9d4271e9a0b4f2f4e5cdbdb04fa29 https://www.encodeproject.org/files/ENCFF587OBC/@@download/ENCFF587OBC.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth biological replicates with identical biosample ENCFF684ASX bed narrowPeak optimal idr thresholded peaks ENCSR000EEC ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MAFF-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF003CWL, ENCFF175OAK, ENCFF611VKE 830843 ENCODE Processing Pipeline 78e68fd09e381d00943cc88af76f83b7 https://www.encodeproject.org/files/ENCFF684ASX/@@download/ENCFF684ASX.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF002CTV bed narrowPeak optimal idr thresholded peaks ENCSR000EEX ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens forskolin and pyruvate 6.0 hour CEBPB-human DNA see document see document False 2011-10-29 ENCODE 354905 ENCODE Consortium Analysis Working Group bb8883f34158c90f74f0db1fbee71fcb https://www.encodeproject.org/files/ENCFF002CTV/@@download/ENCFF002CTV.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF085GOJ bed narrowPeak optimal idr thresholded peaks ENCSR000EEI ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens JUND-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF185JWL, ENCFF716IBZ, ENCFF951EMI 714125 ENCODE Processing Pipeline 88fcc0c2c3af76c5a6ecc6e6f7cc3b2c https://www.encodeproject.org/files/ENCFF085GOJ/@@download/ENCFF085GOJ.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF316NHY bed narrowPeak optimal idr thresholded peaks ENCSR000DXQ ChIP-seq EFO:0003072 SK-N-SH cell line Homo sapiens all-trans-retinoic acid 6 μM 48 hour CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF020JUP, ENCFF359EWI, ENCFF655SOH 815709 ENCODE Processing Pipeline 84970e70aa32e04a1ed816bdb3e001b6 https://www.encodeproject.org/files/ENCFF316NHY/@@download/ENCFF316NHY.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth ENCFF348RKC bed narrowPeak optimal idr thresholded peaks ENCSR000BPE ChIP-seq EFO:0001086 A549 cell line Homo sapiens ethanol 0.02 percent 1 hour SP1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF075ZQI, ENCFF753PAD, ENCFF831GEW 761123 ENCODE Processing Pipeline e5f585bcfb86b66fb3b638e3e0a04b73 https://www.encodeproject.org/files/ENCFF348RKC/@@download/ENCFF348RKC.bed.gz hg19 released low read length biological replicates with identical biosample ENCFF577UJR bed narrowPeak optimal idr thresholded peaks ENCSR000BNV ChIP-seq EFO:0002067 K562 cell line Homo sapiens MEF2A-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF307TQZ, ENCFF435ESC, ENCFF825VQR 22863 ENCODE Processing Pipeline 5e9c735464c7e63dba6ce09405a9eec0 https://www.encodeproject.org/files/ENCFF577UJR/@@download/ENCFF577UJR.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample control insufficient read depth missing control alignments ENCFF002CUB bed narrowPeak optimal idr thresholded peaks ENCSR000EEV ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens forskolin and pyruvate 6.0 hour NR3C1-human DNA see document see document False 2011-10-29 ENCODE 16349 ENCODE Consortium Analysis Working Group 7d2821244ae03f55f8d52105ee912ec3 https://www.encodeproject.org/files/ENCFF002CUB/@@download/ENCFF002CUB.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CMM bed narrowPeak optimal idr thresholded peaks ENCSR000BGX ChIP-seq EFO:0002067 K562 cell line Homo sapiens SIX5-human DNA see document see document False 2011-07-18 ENCODE 94185 ENCODE Consortium Analysis Working Group 1f0494497f4bf36bc3b8cda4c0c37dde https://www.encodeproject.org/files/ENCFF002CMM/@@download/ENCFF002CMM.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF843SYD bed narrowPeak optimal idr thresholded peaks ENCSR000BKK ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens EP300-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF380YEP, ENCFF532VDQ, ENCFF684GVN 241631 ENCODE Processing Pipeline c06ac8027f55d91b669cebbc14184c53 https://www.encodeproject.org/files/ENCFF843SYD/@@download/ENCFF843SYD.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF002CTI bed narrowPeak optimal idr thresholded peaks ENCSR000EDD ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens TBP-human DNA see document see document False 2011-10-29 ENCODE 461868 ENCODE Consortium Analysis Working Group 78449b084d8578fa46731cd08b9efba4 https://www.encodeproject.org/files/ENCFF002CTI/@@download/ENCFF002CTI.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment missing derived_from, biological replicates with identical biosample ENCFF441MEM bed narrowPeak optimal idr thresholded peaks ENCSR000BPX ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 100 nM 1 hour FOXA1-human DNA see document see document False 2012-02-29 ENCODE 1, 2 ENCFF001TDO, ENCFF119XQX, ENCFF432ZAJ, ENCFF953BDX 161662 ENCODE Processing Pipeline 8ae46d4df8dd7ba66eab83564b22fbda https://www.encodeproject.org/files/ENCFF441MEM/@@download/ENCFF441MEM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity, inconsistent target of control experiment biological replicates with identical biosample ENCFF438XHB bed narrowPeak optimal idr thresholded peaks ENCSR000DUU ChIP-seq CL:0002555 fibroblast of mammary gland primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF090XCI, ENCFF681HOI, ENCFF831MNI 812710 ENCODE Processing Pipeline f427a82e1ac58a95b8ba78e63a5fed5b https://www.encodeproject.org/files/ENCFF438XHB/@@download/ENCFF438XHB.bed.gz hg19 released low read length, low read depth, inconsistent platforms control insufficient read depth, insufficient read depth ENCFF365JMJ bed narrowPeak optimal idr thresholded peaks ENCSR000EUN ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens ZNF274-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF015DMU, ENCFF374BCB, ENCFF784FBR 26071 ENCODE Processing Pipeline f96107d880775c7908258193d11e8e3e https://www.encodeproject.org/files/ENCFF365JMJ/@@download/ENCFF365JMJ.bed.gz hg19 released low read length, borderline replicate concordance biological replicates with identical biosample extremely low read depth ENCFF706ISJ bed narrowPeak optimal idr thresholded peaks ENCSR000BME ChIP-seq EFO:0002067 K562 cell line Homo sapiens ZBTB7A-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF101JWH, ENCFF412YTK, ENCFF644MVI 533464 ENCODE Processing Pipeline ee9d4887416c08e558ca9ce0f11d8c69 https://www.encodeproject.org/files/ENCFF706ISJ/@@download/ENCFF706ISJ.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample control insufficient read depth ENCFF002CRM bed narrowPeak optimal idr thresholded peaks ENCSR000EVB ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens ELK4-human DNA see document see document False 2011-10-29 ENCODE 38731 ENCODE Consortium Analysis Working Group 919096356b9185293cad6166f6b760a1 https://www.encodeproject.org/files/ENCFF002CRM/@@download/ENCFF002CRM.bed.gz hg19 released low read length missing derived_from, biological replicates with identical biosample ENCFF732HOE bed narrowPeak optimal idr thresholded peaks ENCSR000EWG ChIP-seq EFO:0002067 K562 cell line Homo sapiens GATA2-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF061TTI, ENCFF163ZFQ, ENCFF717ZNF 185950 ENCODE Processing Pipeline 0a5986cb974e654436fe293de05e5274 https://www.encodeproject.org/files/ENCFF732HOE/@@download/ENCFF732HOE.bed.gz hg19 released biological replicates with identical biosample insufficient read depth, insufficient replicate concordance, insufficient read length ENCFF002CST bed narrowPeak optimal idr thresholded peaks ENCSR000ECU ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens MXI1-human DNA see document see document False 2011-10-29 ENCODE 310642 ENCODE Consortium Analysis Working Group 01dcdbaede61ced878ea89eabffe613c https://www.encodeproject.org/files/ENCFF002CST/@@download/ENCFF002CST.bed.gz hg19 released low read length biological replicates with identical biosample, missing derived_from ENCFF449NOT bed narrowPeak optimal idr thresholded peaks ENCSR000AUV ChIP-seq CL:0000236 B cell primary cell Homo sapiens CTCF-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF209GQK, ENCFF485ZSI, ENCFF603MIK 887114 ENCODE Processing Pipeline 00020b4b010d07d38f7110db620ee494 https://www.encodeproject.org/files/ENCFF449NOT/@@download/ENCFF449NOT.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity missing raw data in replicate missing control alignments ENCFF437LHG bed narrowPeak optimal idr thresholded peaks ENCSR000ATN ChIP-seq CL:0001054 CD14-positive monocyte primary cell Homo sapiens CTCF-human DNA see document see document False 2012-08-06 ENCODE 1, 2 ENCFF001TDO, ENCFF097DFJ, ENCFF446PEN, ENCFF920STO 692739 ENCODE Processing Pipeline d352e31174798d828b982e6429bbb48e https://www.encodeproject.org/files/ENCFF437LHG/@@download/ENCFF437LHG.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity insufficient read depth ENCFF002CSP bed narrowPeak optimal idr thresholded peaks ENCSR000EDH ChIP-seq EFO:0002791 HeLa-S3 cell line Homo sapiens JUND-human DNA see document see document False 2011-10-29 ENCODE 750595 ENCODE Consortium Analysis Working Group 8382b1d2abe95d66c1230cf762e7e99e https://www.encodeproject.org/files/ENCFF002CSP/@@download/ENCFF002CSP.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF002CRP bed narrowPeak optimal idr thresholded peaks ENCSR000EUY ChIP-seq EFO:0001182 HEK293 cell line Homo sapiens TCF7L2-human DNA see document see document False 2011-10-29 ENCODE 227110 ENCODE Consortium Analysis Working Group bb39e8c267d6e62ca145de79bc2057f0 https://www.encodeproject.org/files/ENCFF002CRP/@@download/ENCFF002CRP.bed.gz hg19 released low read length, inconsistent platforms missing derived_from, biological replicates with identical biosample ENCFF168VBK bed narrowPeak optimal idr thresholded peaks ENCSR000DVH ChIP-seq CL:0002518 kidney epithelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF444ZJW, ENCFF536XBD, ENCFF583GIR 708472 ENCODE Processing Pipeline d51a91608457f8beecc7c702e4116d49 https://www.encodeproject.org/files/ENCFF168VBK/@@download/ENCFF168VBK.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth, poor library complexity, severe bottlenecking ENCFF108RWG bed narrowPeak optimal idr thresholded peaks ENCSR000EDT ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens BHLHE40-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF242UCP, ENCFF421CEV, ENCFF919QSI 326205 ENCODE Processing Pipeline fc82e797bbc6c57a75a31c87bf1c63dd https://www.encodeproject.org/files/ENCFF108RWG/@@download/ENCFF108RWG.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF734DZF bed narrowPeak optimal idr thresholded peaks ENCSR000ANO ChIP-seq CL:0002553 fibroblast of lung primary cell Homo sapiens CTCF-human DNA see document see document False 2011-02-10 ENCODE 1, 2 ENCFF001TDO, ENCFF005HNY, ENCFF180IOD, ENCFF579SVE 632017 ENCODE Processing Pipeline 19b0f552c264539be3097aab1fcfe955 https://www.encodeproject.org/files/ENCFF734DZF/@@download/ENCFF734DZF.bed.gz hg19 released control low read depth, low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance poor library complexity, severe bottlenecking extremely low read depth, missing control alignments ENCFF401ONY bed narrowPeak optimal idr thresholded peaks ENCSR000DXI ChIP-seq CL:0002328 bronchial epithelial cell primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF116ONS, ENCFF453SOO, ENCFF821CAK 707859 ENCODE Processing Pipeline bd9ebf6bcf664839e8f8464a465ebea0 https://www.encodeproject.org/files/ENCFF401ONY/@@download/ENCFF401ONY.bed.gz hg19 released control low read depth, low read length, mild to moderate bottlenecking, inconsistent platforms, moderate library complexity insufficient read depth, severe bottlenecking extremely low read depth ENCFF648ZNE bed narrowPeak optimal idr thresholded peaks ENCSR000BHF ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 50 nM 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF185AVK, ENCFF424TUG, ENCFF680RJL 458466 ENCODE Processing Pipeline 3e28d89d949807a1ffc27397ebde933f https://www.encodeproject.org/files/ENCFF648ZNE/@@download/ENCFF648ZNE.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample ENCFF681OWQ bed narrowPeak optimal idr thresholded peaks ENCSR000DPM ChIP-seq EFO:0006270 AG04450 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 1, 2 ENCFF001TDO, ENCFF121QUN, ENCFF709XOM, ENCFF940KDS 780687 ENCODE Processing Pipeline 9785a54dd69bb39cb46f95c625e0c1fb https://www.encodeproject.org/files/ENCFF681OWQ/@@download/ENCFF681OWQ.bed.gz hg19 released control low read depth, low read length, low read depth, inconsistent platforms ENCFF646GCM bed narrowPeak optimal idr thresholded peaks ENCSR000EBS ChIP-seq EFO:0003042 H1-hESC stem cell Homo sapiens MAFK-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF039SJR, ENCFF671DTY, ENCFF977JIT 237494 ENCODE Processing Pipeline 108afcdf21f46b3d015de451be0f4d11 https://www.encodeproject.org/files/ENCFF646GCM/@@download/ENCFF646GCM.bed.gz hg19 released file validation error, low read length, mild to moderate bottlenecking, low read depth, inconsistent target of control experiment biological replicates with identical biosample, mismatched file status ENCFF002DAJ bed narrowPeak optimal idr thresholded peaks ENCSR000DKV ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 943769 ENCODE Consortium Analysis Working Group f05d542a177ee7a769c68a1f4e553b67 https://www.encodeproject.org/files/ENCFF002DAJ/@@download/ENCFF002DAJ.bed.gz hg19 released inconsistent platforms missing derived_from, biological replicates with identical biosample insufficient read length ENCFF269JRM bed narrowPeak optimal idr thresholded peaks ENCSR000EXZ ChIP-seq EFO:0002717 SH-SY5Y cell line Homo sapiens GATA3-human DNA see document see document False 2011-10-29 ENCODE 1, 2 ENCFF001TDO, ENCFF272ARC, ENCFF601TVP, ENCFF646DRT 345418 ENCODE Processing Pipeline 3ab06a65b20e88ae95e4e386e2a9a886 https://www.encodeproject.org/files/ENCFF269JRM/@@download/ENCFF269JRM.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, moderate library complexity biological replicates with identical biosample ENCFF132WOI bed narrowPeak optimal idr thresholded peaks ENCSR000BKY ChIP-seq EFO:0001247 T47D cell line Homo sapiens dimethyl sulfoxide 0.02 percent 1 hour FOXA1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF038SPJ, ENCFF526YXC, ENCFF544QLN 811564 ENCODE Processing Pipeline ba6fe4d9eb5bab786a9c237bd412de9f https://www.encodeproject.org/files/ENCFF132WOI/@@download/ENCFF132WOI.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF002DBA bed narrowPeak optimal idr thresholded peaks ENCSR000DLW ChIP-seq CL:0002618 endothelial cell of umbilical vein primary cell Homo sapiens CTCF-human DNA see document see document False 2011-03-17 ENCODE 891419 ENCODE Consortium Analysis Working Group d488647dab782e3362984b6656a72d0b https://www.encodeproject.org/files/ENCFF002DBA/@@download/ENCFF002DBA.bed.gz hg19 released biological replicates with identical biosample, missing derived_from insufficient read length ENCFF421SEJ bed narrowPeak optimal idr thresholded peaks ENCSR000EDN ChIP-seq EFO:0001187 HepG2 cell line Homo sapiens MAZ-human DNA see document see document False 2012-05-14 ENCODE 1, 2 ENCFF001TDO, ENCFF479LKN, ENCFF668ITU, ENCFF969CUT 285287 ENCODE Processing Pipeline 5b4317e08a15d3d41a087c68fcdcf641 https://www.encodeproject.org/files/ENCFF421SEJ/@@download/ENCFF421SEJ.bed.gz hg19 released borderline replicate concordance, moderate library complexity, inconsistent target of control experiment, low read length, mild to moderate bottlenecking, low read depth biological replicates with identical biosample ENCFF721SDD bed narrowPeak optimal idr thresholded peaks ENCSR000DYR ChIP-seq EFO:0002784 GM12878 cell line Homo sapiens CUX1-human DNA see document see document False 2012-08-20 ENCODE 1, 2 ENCFF001TDO, ENCFF253OOR, ENCFF452BDW, ENCFF881ZSX 144927 ENCODE Processing Pipeline 2baa963f5a20127cf4c51d1458e74e6f https://www.encodeproject.org/files/ENCFF721SDD/@@download/ENCFF721SDD.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient replicate concordance ENCFF917ZPO bed narrowPeak optimal idr thresholded peaks ENCSR000BSE ChIP-seq EFO:0002824 HCT116 cell line Homo sapiens CTCF-human DNA see document see document False 2012-09-10 ENCODE 1, 2 ENCFF001TDO, ENCFF021NMZ, ENCFF214AAT, ENCFF971PWB 602672 ENCODE Processing Pipeline eb204541dbdac5aa54d530917f198a18 https://www.encodeproject.org/files/ENCFF917ZPO/@@download/ENCFF917ZPO.bed.gz hg19 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, moderate library complexity biological replicates with identical biosample insufficient read depth missing control alignments ENCFF080RMP bed narrowPeak optimal idr thresholded peaks ENCSR000BJR ChIP-seq EFO:0001086 A549 cell line Homo sapiens dexamethasone 100 nM 1 hour NR3C1-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF033RSK, ENCFF631NXF, ENCFF664XHQ 222072 ENCODE Processing Pipeline cf7d2954902a39818ff7b875dc307a9e https://www.encodeproject.org/files/ENCFF080RMP/@@download/ENCFF080RMP.bed.gz hg19 released low read length, low read depth, inconsistent target of control experiment biological replicates with identical biosample insufficient read depth ENCFF475TQE bed narrowPeak optimal idr thresholded peaks ENCSR000BNU ChIP-seq EFO:0002067 K562 cell line Homo sapiens ATF3-human DNA see document see document False 2011-07-18 ENCODE 1, 2 ENCFF001TDO, ENCFF015HEH, ENCFF146YXX, ENCFF251XOI 128953 ENCODE Processing Pipeline 146c148cf8221517c340d416403eefc1 https://www.encodeproject.org/files/ENCFF475TQE/@@download/ENCFF475TQE.bed.gz hg19 released low read length, mild to moderate bottlenecking, low read depth, borderline replicate concordance, moderate library complexity biological replicates with identical biosample control insufficient read depth