ENCFF972VNL bed narrowPeak optimal idr thresholded peaks ENCSR000DIM ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF266CYV, ENCFF547MET, ENCFF827ERW, ENCFF974KFZ 55241 ENCODE Processing Pipeline d0e560eda821c03589cef1594aed7215 https://www.encodeproject.org/files/ENCFF972VNL/@@download/ENCFF972VNL.bed.gz mm10 released low read length, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF648DAC bed narrowPeak optimal idr thresholded peaks ENCSR000CBM ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF091ZMO, ENCFF284DTM, ENCFF547MET, ENCFF731OCE 295782 ENCODE Processing Pipeline c8a94e6a8f9e26fb18c92d29736b8c98 https://www.encodeproject.org/files/ENCFF648DAC/@@download/ENCFF648DAC.bed.gz mm10 released borderline replicate concordance, low read length, mild to moderate bottlenecking, control low read depth, low read depth insufficient read depth, control insufficient read depth ENCFF048VNT bed narrowPeak optimal idr thresholded peaks ENCSR041SMK ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF057OUB, ENCFF310FWM, ENCFF547MET, ENCFF708ZJC 912745 ENCODE Processing Pipeline a469d67bd20bc36a1ede7f44f7a05567 https://www.encodeproject.org/files/ENCFF048VNT/@@download/ENCFF048VNT.bed.gz mm10 released antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF945WJZ bed narrowPeak optimal idr thresholded peaks ENCSR000CBX ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF285RDR, ENCFF496XMO, ENCFF547MET, ENCFF741HGT 501803 ENCODE Processing Pipeline 3537a6ecae7ae45e84420d2a443875e2 https://www.encodeproject.org/files/ENCFF945WJZ/@@download/ENCFF945WJZ.bed.gz mm10 released low read length, mild to moderate bottlenecking, moderate library complexity, control low read depth, low read depth ENCFF645WRI bed narrowPeak optimal idr thresholded peaks ENCSR000ERC ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus BHLHE40-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF065TVE, ENCFF547MET, ENCFF647KNH, ENCFF918DGZ 822744 ENCODE Processing Pipeline 868982edc07ebcd6523a7f5f84f1b431 https://www.encodeproject.org/files/ENCFF645WRI/@@download/ENCFF645WRI.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth duplicate lane review ENCFF752ZTC bed narrowPeak optimal idr thresholded peaks ENCSR000DIP ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF103KWB, ENCFF439LAM, ENCFF547MET, ENCFF688HQL 548057 ENCODE Processing Pipeline 8cb3df5c51199a58d6fdaa05100139f4 https://www.encodeproject.org/files/ENCFF752ZTC/@@download/ENCFF752ZTC.bed.gz mm10 released mixed read lengths, low read length, inconsistent platforms, low read depth ENCFF580LNR bed narrowPeak optimal idr thresholded peaks ENCSR677HXC ChIP-seq UBERON:0001890 forebrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF547MET, ENCFF720THG, ENCFF779QUY, ENCFF857UVO 894734 ENCODE Processing Pipeline 64bff7c334186c4ebe0fabf64abaf7d2 https://www.encodeproject.org/files/ENCFF580LNR/@@download/ENCFF580LNR.bed.gz mm10 released control low read depth, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF320ZSC bed narrowPeak optimal idr thresholded peaks ENCSR777VNA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1, 2 ENCFF499JRK, ENCFF547MET, ENCFF563DIX, ENCFF771SCO 320977 ENCODE Processing Pipeline 0f513be9893c8de8f73b61ec1d824f37 https://www.encodeproject.org/files/ENCFF320ZSC/@@download/ENCFF320ZSC.bed.gz mm10 released antibody characterized with exemption, low read depth biological replicates with identical biosample ENCFF457CXR bed narrowPeak optimal idr thresholded peaks ENCSR000ERR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUND-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF547MET, ENCFF563YXX, ENCFF887GRQ, ENCFF908CAW 327634 ENCODE Processing Pipeline 4c1b07b9bc2d795612bcd4afb3474b55 https://www.encodeproject.org/files/ENCFF457CXR/@@download/ENCFF457CXR.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF054PAU bed narrowPeak optimal idr thresholded peaks ENCSR000ETB ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ETS1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF281XVX, ENCFF446YOW, ENCFF547MET, ENCFF827MBR 736214 ENCODE Processing Pipeline e3802873a4c17c362ce5ea734845d1f1 https://www.encodeproject.org/files/ENCFF054PAU/@@download/ENCFF054PAU.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample ENCFF377JTE bed narrowPeak optimal idr thresholded peaks ENCSR000ERW ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF507SGS, ENCFF547MET, ENCFF629JWT, ENCFF929BUB 330877 ENCODE Processing Pipeline 883cffa8d63a81203d08d23ba268e5e4 https://www.encodeproject.org/files/ENCFF377JTE/@@download/ENCFF377JTE.bed.gz mm10 released borderline replicate concordance, low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF611SZM bed narrowPeak optimal idr thresholded peaks ENCSR000ESD ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF257UCC, ENCFF439TXC, ENCFF547MET, ENCFF665RZK 605216 ENCODE Processing Pipeline 04885dbeb322e6acf18ef60d9e78a068 https://www.encodeproject.org/files/ENCFF611SZM/@@download/ENCFF611SZM.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF976DPO bed narrowPeak optimal idr thresholded peaks ENCSR000DIS ChIP-seq EFO:0002034 G1E stem cell Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF547MET, ENCFF925MJG, ENCFF957QMK, ENCFF983MKP 272466 ENCODE Processing Pipeline 2853e82cc05b43e058e0d2458deb89a0 https://www.encodeproject.org/files/ENCFF976DPO/@@download/ENCFF976DPO.bed.gz mm10 released mixed read lengths, low read length, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF739OMJ bed narrowPeak optimal idr thresholded peaks ENCSR000ERM ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF021GBR, ENCFF547MET, ENCFF720ZXB, ENCFF892SBI 1030359 ENCODE Processing Pipeline e9525ea80812e160b7f33e45dfeed555 https://www.encodeproject.org/files/ENCFF739OMJ/@@download/ENCFF739OMJ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth ENCFF235LMU bed narrowPeak optimal idr thresholded peaks ENCSR000ETE ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus dimethyl sulfoxide 2 percent 5 day CTCF-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF406PTJ, ENCFF547MET, ENCFF855DZF, ENCFF957XPC 677637 ENCODE Processing Pipeline bfe9bbfe82c380439b73ca07c830ff17 https://www.encodeproject.org/files/ENCFF235LMU/@@download/ENCFF235LMU.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF806PDR bed narrowPeak optimal idr thresholded peaks ENCSR000CBL ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF547MET, ENCFF774XDZ, ENCFF846ENI, ENCFF900XVJ 449965 ENCODE Processing Pipeline ea223ed654bbe195a05dedec31ac60cc https://www.encodeproject.org/files/ENCFF806PDR/@@download/ENCFF806PDR.bed.gz mm10 released low read length, control low read depth insufficient read depth, control insufficient read depth ENCFF946EZQ bed narrowPeak optimal idr thresholded peaks ENCSR000ETS ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus RAD21-mouse DNA see document see document False 2011-02-07 ENCODE 1, 2 ENCFF213KTF, ENCFF256IES, ENCFF426BMQ, ENCFF547MET 549585 ENCODE Processing Pipeline ea84c4721c69c7b5eb4e61e07f28cd9e https://www.encodeproject.org/files/ENCFF946EZQ/@@download/ENCFF946EZQ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF151IMU bed narrowPeak optimal idr thresholded peaks ENCSR000DHD ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus FLI1-mouse DNA see document see document False 2012-08-07 ENCODE 1, 2 ENCFF082ZXF, ENCFF547MET, ENCFF630ESV, ENCFF790TJE 62273 ENCODE Processing Pipeline 8378edf484528fc351de285d63306e8e https://www.encodeproject.org/files/ENCFF151IMU/@@download/ENCFF151IMU.bed.gz mm10 released low read length, inconsistent platforms, mixed read lengths NTR biosample, biological replicates with identical biosample ENCFF049FSZ bed narrowPeak optimal idr thresholded peaks ENCSR000EQQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF160QIJ, ENCFF538CFM, ENCFF547MET, ENCFF592TWQ 172863 ENCODE Processing Pipeline 0a1a52670f4c14edd6a2538541861e87 https://www.encodeproject.org/files/ENCFF049FSZ/@@download/ENCFF049FSZ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF565YYF bed narrowPeak optimal idr thresholded peaks ENCSR000DID ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour GATA2-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF265CLS, ENCFF547MET, ENCFF800RBP, ENCFF936PNG 6171 ENCODE Processing Pipeline 06efade9a272737e19815745652f0097 https://www.encodeproject.org/files/ENCFF565YYF/@@download/ENCFF565YYF.bed.gz mm10 released low read length, inconsistent platforms biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF168IVP bed narrowPeak optimal idr thresholded peaks ENCSR000CFH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF041ZCF, ENCFF547MET, ENCFF641UWK, ENCFF953YSC 571353 ENCODE Processing Pipeline 857d97eb1970552f17bdab0069091f90 https://www.encodeproject.org/files/ENCFF168IVP/@@download/ENCFF168IVP.bed.gz mm10 released low read length, mild to moderate bottlenecking insufficient read depth, severe bottlenecking, poor library complexity, control insufficient read depth ENCFF875LZX bed narrowPeak optimal idr thresholded peaks ENCSR765RPR ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1, 2 ENCFF098DOF, ENCFF534RWN, ENCFF547MET, ENCFF619GPG 475161 ENCODE Processing Pipeline aab17bd690e9f6da9619fdce6330b377 https://www.encodeproject.org/files/ENCFF875LZX/@@download/ENCFF875LZX.bed.gz mm10 released mild to moderate bottlenecking, antibody characterized with exemption, low read depth biological replicates with identical biosample ENCFF237TCV bed narrowPeak optimal idr thresholded peaks ENCSR000DIC ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF193XWY, ENCFF327RPY, ENCFF547MET, ENCFF716MDN 951 ENCODE Processing Pipeline d2d8ad09a8285b91c3b020978fb39c95 https://www.encodeproject.org/files/ENCFF237TCV/@@download/ENCFF237TCV.bed.gz mm10 released mixed read lengths, low read length, inconsistent platforms, borderline replicate concordance biological replicates with identical biosample ENCFF633EAU bed narrowPeak optimal idr thresholded peaks ENCSR000ESJ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus UBTF-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF261QKD, ENCFF547MET, ENCFF625GKR, ENCFF998UBT 129470 ENCODE Processing Pipeline 935cc47905af07cb1433dc0cb5a00845 https://www.encodeproject.org/files/ENCFF633EAU/@@download/ENCFF633EAU.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample insufficient read depth ENCFF906DFS bed narrowPeak optimal idr thresholded peaks ENCSR000EQT ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAZ-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF268WMK, ENCFF334SDJ, ENCFF436RKB, ENCFF547MET 393347 ENCODE Processing Pipeline 8266a5880dae3cfafd756d4afe6e307e https://www.encodeproject.org/files/ENCFF906DFS/@@download/ENCFF906DFS.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity ENCFF039DWK bed narrowPeak optimal idr thresholded peaks ENCSR000CFI ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF007TXO, ENCFF388WCL, ENCFF547MET, ENCFF941FIA 301620 ENCODE Processing Pipeline 0e2cb01687976da10bfa79b0b3f2fc35 https://www.encodeproject.org/files/ENCFF039DWK/@@download/ENCFF039DWK.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth insufficient read depth, poor library complexity, control insufficient read depth ENCFF006XAF bed narrowPeak optimal idr thresholded peaks ENCSR000ESY ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus dimethyl sulfoxide 2 percent 5 day MAFK-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF150XOB, ENCFF247AEB, ENCFF344XYS, ENCFF547MET 45946 ENCODE Processing Pipeline 795bf3ba1591336cc40547541f118ee2 https://www.encodeproject.org/files/ENCFF006XAF/@@download/ENCFF006XAF.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF132DDY bed narrowPeak optimal idr thresholded peaks ENCSR450KVW ChIP-seq UBERON:0000945 stomach tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1, 2 ENCFF477NPU, ENCFF487STG, ENCFF547MET, ENCFF687GFY 147487 ENCODE Processing Pipeline b37b7917a9265733283388c8502c8b01 https://www.encodeproject.org/files/ENCFF132DDY/@@download/ENCFF132DDY.bed.gz mm10 released antibody characterized with exemption biological replicates with identical biosample ENCFF542WEE bed narrowPeak optimal idr thresholded peaks ENCSR000CBU ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF371UBQ, ENCFF547MET, ENCFF676VZW, ENCFF930JOQ 592190 ENCODE Processing Pipeline 485442bbbd097f4298f1472654f4e7f6 https://www.encodeproject.org/files/ENCFF542WEE/@@download/ENCFF542WEE.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth, low read depth insufficient read depth ENCFF458TAP bed narrowPeak optimal idr thresholded peaks ENCSR000CBR ChIP-seq UBERON:0002107 liver tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF125NGA, ENCFF547MET, ENCFF720XKE, ENCFF730SNE 228733 ENCODE Processing Pipeline 8e0f5fe0bcaabf2e70557b241f681914 https://www.encodeproject.org/files/ENCFF458TAP/@@download/ENCFF458TAP.bed.gz mm10 released low read length, control low read depth insufficient read depth extremely low read depth ENCFF627TGO bed narrowPeak optimal idr thresholded peaks ENCSR000ESK ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus GABPA-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF101AMR, ENCFF378SRR, ENCFF547MET, ENCFF890BUV 58993 ENCODE Processing Pipeline 1647fb66fc3e5d064d9fa0407b687ebf https://www.encodeproject.org/files/ENCFF627TGO/@@download/ENCFF627TGO.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample ENCFF691HWC bed narrowPeak optimal idr thresholded peaks ENCSR000DIN ChIP-seq EFO:0002034 G1E stem cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF037UNY, ENCFF461KXI, ENCFF547MET, ENCFF578SUN 132433 ENCODE Processing Pipeline b0217e14217025e90d9f7a5e014f0a30 https://www.encodeproject.org/files/ENCFF691HWC/@@download/ENCFF691HWC.bed.gz mm10 released mixed read lengths, low read length, inconsistent platforms, low read depth biological replicates with identical biosample insufficient read depth ENCFF609NWN bed narrowPeak optimal idr thresholded peaks ENCSR392DGA ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus POU5F1-mouse DNA see document see document False 2014-03-17 ENCODE 1, 2 ENCFF238TDR, ENCFF403ZTD, ENCFF417EAQ, ENCFF547MET 70748 ENCODE Processing Pipeline d16843514657d5af3a155a0cb2fc8739 https://www.encodeproject.org/files/ENCFF609NWN/@@download/ENCFF609NWN.bed.gz mm10 released low read length, borderline replicate concordance experiment not submitted to GEO ENCFF433SGC bed narrowPeak optimal idr thresholded peaks ENCSR000DHZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF226EPH, ENCFF242JJL, ENCFF547MET, ENCFF702KXH 99692 ENCODE Processing Pipeline eec6085cda68d73adddb7baf3c50ef15 https://www.encodeproject.org/files/ENCFF433SGC/@@download/ENCFF433SGC.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, mixed read lengths, low read depth, inconsistent platforms, low read length ENCFF508CKL bed narrowPeak optimal idr thresholded peaks ENCSR000CCB ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF229BOI, ENCFF520LES, ENCFF547MET, ENCFF634ZNO 662595 ENCODE Processing Pipeline 47204ccf6b524aae64a0e776b25956aa https://www.encodeproject.org/files/ENCFF508CKL/@@download/ENCFF508CKL.bed.gz mm10 released low read length insufficient read depth ENCFF751UTU bed narrowPeak optimal idr thresholded peaks ENCSR000ERI ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus EP300-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF293RPG, ENCFF547MET, ENCFF560XGM, ENCFF887HXT 656135 ENCODE Processing Pipeline b13da342359a3858d46027fd5e9fb4f4 https://www.encodeproject.org/files/ENCFF751UTU/@@download/ENCFF751UTU.bed.gz mm10 released low read length, inconsistent target of control experiment ENCFF311HPG bed narrowPeak optimal idr thresholded peaks ENCSR000CBJ ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF258WBW, ENCFF523FYC, ENCFF547MET, ENCFF601AJL 606640 ENCODE Processing Pipeline e69e7c9495ae7b1486a52239b52c3afb https://www.encodeproject.org/files/ENCFF311HPG/@@download/ENCFF311HPG.bed.gz mm10 released mild to moderate bottlenecking, mixed read lengths, low read depth, control low read depth, low read length, moderate library complexity insufficient read depth, insufficient read length ENCFF305VBR bed narrowPeak optimal idr thresholded peaks ENCSR000ERF ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD2-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF030WPJ, ENCFF337BFS, ENCFF433YEA, ENCFF547MET 404497 ENCODE Processing Pipeline 3a1fe51a2e6f8e6fbbe2204d95d855f0 https://www.encodeproject.org/files/ENCFF305VBR/@@download/ENCFF305VBR.bed.gz mm10 released low read length, inconsistent target of control experiment ENCFF454MFZ bed narrowPeak optimal idr thresholded peaks ENCSR000CBS ChIP-seq UBERON:0000948 heart tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF270RGP, ENCFF466TIE, ENCFF547MET, ENCFF838VJB 467428 ENCODE Processing Pipeline 632f1826ff37c9254f1d75dabed59a86 https://www.encodeproject.org/files/ENCFF454MFZ/@@download/ENCFF454MFZ.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth insufficient read depth ENCFF500CDH bed narrowPeak optimal idr thresholded peaks ENCSR000CBZ ChIP-seq UBERON:0002106 spleen tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF518LVB, ENCFF547MET, ENCFF555WTT, ENCFF585YDB 167457 ENCODE Processing Pipeline 4f82008b81e781adea9a653694afcf76 https://www.encodeproject.org/files/ENCFF500CDH/@@download/ENCFF500CDH.bed.gz mm10 released low read length, inconsistent platforms, low read depth ENCFF722CPN bed narrowPeak optimal idr thresholded peaks ENCSR000ERX ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF199OAD, ENCFF431QAW, ENCFF547MET, ENCFF622XHL 207209 ENCODE Processing Pipeline 29ec5d4f84340fa8a01b6b9475a08ade https://www.encodeproject.org/files/ENCFF722CPN/@@download/ENCFF722CPN.bed.gz mm10 released low read length, inconsistent platforms, borderline replicate concordance biological replicates with identical biosample insufficient read depth ENCFF265CAB bed narrowPeak optimal idr thresholded peaks ENCSR000EQV ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF063TGF, ENCFF513MBD, ENCFF547MET, ENCFF750VUM 331303 ENCODE Processing Pipeline 8a8ad31a532c1f2279298bd5459a50a9 https://www.encodeproject.org/files/ENCFF265CAB/@@download/ENCFF265CAB.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF267LBA bed narrowPeak optimal idr thresholded peaks ENCSR000DIF ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 1, 3 ENCFF157PDK, ENCFF223DYF, ENCFF547MET, ENCFF832MGP 13967 ENCODE Processing Pipeline 16b8ba3ddd006eb0e9cf4db606eff289 https://www.encodeproject.org/files/ENCFF267LBA/@@download/ENCFF267LBA.bed.gz mm10 released low read length, inconsistent platforms, low read depth missing raw data in replicate, biological replicates with identical biosample ENCFF402YZT bed narrowPeak optimal idr thresholded peaks ENCSR000ERG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SMC3-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF275BHY, ENCFF431GLY, ENCFF490BZL, ENCFF547MET 758228 ENCODE Processing Pipeline 84f51d843d33a64b8f96bb8a130c1067 https://www.encodeproject.org/files/ENCFF402YZT/@@download/ENCFF402YZT.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF283XCT bed narrowPeak optimal idr thresholded peaks ENCSR104QEN ChIP-seq UBERON:0000945 stomach tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF104PYP, ENCFF547MET, ENCFF686MBJ, ENCFF880QHG 1193732 ENCODE Processing Pipeline d4c5cfb2455bb43afd656c8b8b4bc646 https://www.encodeproject.org/files/ENCFF283XCT/@@download/ENCFF283XCT.bed.gz mm10 released moderate library complexity, mild to moderate bottlenecking, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF784YSO bed narrowPeak optimal idr thresholded peaks ENCSR143WOK ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF381LLL, ENCFF408VND, ENCFF547MET, ENCFF694LLR 1043514 ENCODE Processing Pipeline db9ea3d68f32df3614efaf7db13de409 https://www.encodeproject.org/files/ENCFF784YSO/@@download/ENCFF784YSO.bed.gz mm10 released moderate library complexity, mild to moderate bottlenecking, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF235YHK bed narrowPeak optimal idr thresholded peaks ENCSR000ESF ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF273QJV, ENCFF547MET, ENCFF628USD, ENCFF715AQW 385653 ENCODE Processing Pipeline 7680aaf37ea7486439262f5660a821a3 https://www.encodeproject.org/files/ENCFF235YHK/@@download/ENCFF235YHK.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF057GJF bed narrowPeak optimal idr thresholded peaks ENCSR985ZTV ChIP-seq UBERON:0001891 midbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF039DHV, ENCFF169BDL, ENCFF547MET, ENCFF726SOK 1083288 ENCODE Processing Pipeline 4d47e1a1b466b510769fd75fbead8492 https://www.encodeproject.org/files/ENCFF057GJF/@@download/ENCFF057GJF.bed.gz mm10 released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF332QLW bed narrowPeak optimal idr thresholded peaks ENCSR397RHW ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF449LBJ, ENCFF547MET, ENCFF587JOJ, ENCFF689ZFH 828425 ENCODE Processing Pipeline c50d9c738cf0414af6fbf5275be99b53 https://www.encodeproject.org/files/ENCFF332QLW/@@download/ENCFF332QLW.bed.gz mm10 released control low read depth, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF839UAT bed narrowPeak optimal idr thresholded peaks ENCSR000ESE ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZMIZ1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF547MET, ENCFF601QJA, ENCFF671FLC, ENCFF671KJV 304759 ENCODE Processing Pipeline ff28ac624c17e2e88ceb4906fea87265 https://www.encodeproject.org/files/ENCFF839UAT/@@download/ENCFF839UAT.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample ENCFF987CNG bed narrowPeak optimal idr thresholded peaks ENCSR000ETU ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus NELFE-mouse DNA see document see document False 2011-02-07 ENCODE 1, 2 ENCFF166NPN, ENCFF179HMP, ENCFF188WWN, ENCFF547MET 429279 ENCODE Processing Pipeline f62afc84822e9410855ed49187653559 https://www.encodeproject.org/files/ENCFF987CNG/@@download/ENCFF987CNG.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF737UCD bed narrowPeak optimal idr thresholded peaks ENCSR000EQZ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RCOR1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF015NGN, ENCFF125MUD, ENCFF547MET, ENCFF982BHY 245870 ENCODE Processing Pipeline be36fb4686aa2c84539dd2fcc5ba6964 https://www.encodeproject.org/files/ENCFF737UCD/@@download/ENCFF737UCD.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment ENCFF074DVX bed narrowPeak optimal idr thresholded peaks ENCSR002ZAG ChIP-seq UBERON:0000160 intestine tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF179SMD, ENCFF445WGT, ENCFF547MET, ENCFF934ACG 1173213 ENCODE Processing Pipeline c94fd16c74a71bbc5845c38311107108 https://www.encodeproject.org/files/ENCFF074DVX/@@download/ENCFF074DVX.bed.gz mm10 released antibody characterized with exemption, moderate library complexity, mild to moderate bottlenecking, control low read depth, low read depth NTR biosample, biological replicates with identical biosample ENCFF252SAA bed narrowPeak optimal idr thresholded peaks ENCSR000CDY ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF272CKS, ENCFF458VDY, ENCFF547MET, ENCFF855XCG 246128 ENCODE Processing Pipeline 9e9373f5a7492124121909579ccab211 https://www.encodeproject.org/files/ENCFF252SAA/@@download/ENCFF252SAA.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking insufficient read depth ENCFF223ASW bed narrowPeak optimal idr thresholded peaks ENCSR000ETQ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF543BMO, ENCFF547MET, ENCFF583EGX, ENCFF958LHR 775076 ENCODE Processing Pipeline 48f656a23d53b1ca1c828da1ffe3a066 https://www.encodeproject.org/files/ENCFF223ASW/@@download/ENCFF223ASW.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF112IBI bed narrowPeak optimal idr thresholded peaks ENCSR000DIU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF173SFG, ENCFF210RNE, ENCFF547MET, ENCFF844FUF 433324 ENCODE Processing Pipeline c6fb1e9f83feb30317b951668b09b110 https://www.encodeproject.org/files/ENCFF112IBI/@@download/ENCFF112IBI.bed.gz mm10 released low read length, inconsistent platforms, low read depth ENCFF624HQU bed narrowPeak optimal idr thresholded peaks ENCSR000ETY ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus E2F4-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF065JNG, ENCFF289QRZ, ENCFF334JLD, ENCFF547MET 92029 ENCODE Processing Pipeline 83a772de8b10e4c2dd0f4a93aecf6805 https://www.encodeproject.org/files/ENCFF624HQU/@@download/ENCFF624HQU.bed.gz mm10 released borderline replicate concordance, low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF473GQJ bed narrowPeak optimal idr thresholded peaks ENCSR000ETN ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MXI1-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF019YYF, ENCFF060SFQ, ENCFF547MET, ENCFF745WHA 731093 ENCODE Processing Pipeline 0d2b8c6d083a873f54e06433cf2ad03a https://www.encodeproject.org/files/ENCFF473GQJ/@@download/ENCFF473GQJ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF290WGR bed narrowPeak optimal idr thresholded peaks ENCSR000ERB ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAFK-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF085OPN, ENCFF547MET, ENCFF809MLM, ENCFF893RVJ 390830 ENCODE Processing Pipeline d64150a52d887cc55594e77461446ee1 https://www.encodeproject.org/files/ENCFF290WGR/@@download/ENCFF290WGR.bed.gz mm10 released low read length, inconsistent target of control experiment, borderline replicate concordance ENCFF305FHK bed narrowPeak optimal idr thresholded peaks ENCSR000EQU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus KAT2A-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF456RMG, ENCFF519AAU, ENCFF547MET, ENCFF585PZU 225029 ENCODE Processing Pipeline 62f34e97c52ee49f5b5bc81d182f5407 https://www.encodeproject.org/files/ENCFF305FHK/@@download/ENCFF305FHK.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment, low read depth insufficient replicate concordance ENCFF672FKP bed narrowPeak optimal idr thresholded peaks ENCSR000ESM ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus KAT2A-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF262YAQ, ENCFF375ZYJ, ENCFF547MET, ENCFF699YLJ 122568 ENCODE Processing Pipeline 39c3f442a8640ad8caff33646eca95d6 https://www.encodeproject.org/files/ENCFF672FKP/@@download/ENCFF672FKP.bed.gz mm10 released borderline replicate concordance, low read length, inconsistent platforms, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF787DRX bed narrowPeak optimal idr thresholded peaks ENCSR982LJQ ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1, 2 ENCFF184GHO, ENCFF514IKI, ENCFF547MET, ENCFF845YIG 300441 ENCODE Processing Pipeline 9d0f2b10155454b870c0e7d1d1b2b776 https://www.encodeproject.org/files/ENCFF787DRX/@@download/ENCFF787DRX.bed.gz mm10 released antibody characterized with exemption, low read depth biological replicates with identical biosample ENCFF308FHB bed narrowPeak optimal idr thresholded peaks ENCSR150RGT ChIP-seq UBERON:0002028 hindbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF036ACY, ENCFF242NJN, ENCFF547MET, ENCFF636SDF 1008807 ENCODE Processing Pipeline 18c6f76162003817c8615d42b2228fbe https://www.encodeproject.org/files/ENCFF308FHB/@@download/ENCFF308FHB.bed.gz mm10 released control low read depth, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF691ZAR bed narrowPeak optimal idr thresholded peaks ENCSR000ERK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RAD21-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF301ZTS, ENCFF534XMO, ENCFF547MET, ENCFF641HGZ 1009902 ENCODE Processing Pipeline e579ff40e4602aac7987dabb55426151 https://www.encodeproject.org/files/ENCFF691ZAR/@@download/ENCFF691ZAR.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth ENCFF047ODZ bed narrowPeak optimal idr thresholded peaks ENCSR000DIA ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF274VSJ, ENCFF547MET, ENCFF704SPV, ENCFF831EXK 311461 ENCODE Processing Pipeline 371c46e26088049fa7b40b4ae83b0002 https://www.encodeproject.org/files/ENCFF047ODZ/@@download/ENCFF047ODZ.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms, mixed read lengths ENCFF714WDP bed narrowPeak optimal idr thresholded peaks ENCSR000CDZ ChIP-seq UBERON:0002370 thymus tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF036INA, ENCFF547MET, ENCFF659CTO, ENCFF897WQO 326073 ENCODE Processing Pipeline 61e2493535ae361665ef23aedbd29310 https://www.encodeproject.org/files/ENCFF714WDP/@@download/ENCFF714WDP.bed.gz mm10 released low read length, mild to moderate bottlenecking, moderate library complexity, control low read depth, borderline replicate concordance insufficient read depth, poor library complexity, control insufficient read depth extremely low read depth ENCFF409RRE bed narrowPeak optimal idr thresholded peaks ENCSR491NUM ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF107KOO, ENCFF139WDG, ENCFF157SGS, ENCFF547MET 703430 ENCODE Processing Pipeline 44f9968428b833e87a382501c377e2d1 https://www.encodeproject.org/files/ENCFF409RRE/@@download/ENCFF409RRE.bed.gz mm10 released control low read depth, antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF125PID bed narrowPeak optimal idr thresholded peaks ENCSR000ERQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2A-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF189GIV, ENCFF351WCO, ENCFF404OWN, ENCFF547MET 545905 ENCODE Processing Pipeline 0cc9791c704957ab32653bf5c161195f https://www.encodeproject.org/files/ENCFF125PID/@@download/ENCFF125PID.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth ENCFF647MPR bed narrowPeak optimal idr thresholded peaks ENCSR000ESL ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAZ-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF177BJJ, ENCFF520IHS, ENCFF547MET, ENCFF551YJH 380295 ENCODE Processing Pipeline f125cafb194dd7d0f5b67a55ae32d588 https://www.encodeproject.org/files/ENCFF647MPR/@@download/ENCFF647MPR.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF474YPG bed narrowPeak optimal idr thresholded peaks ENCSR000CEE ChIP-seq UBERON:0002108 small intestine tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF402RSB, ENCFF547MET, ENCFF687OPD, ENCFF968EUZ 268169 ENCODE Processing Pipeline ed45219ec5b2e5f0ed7173080aa14ff9 https://www.encodeproject.org/files/ENCFF474YPG/@@download/ENCFF474YPG.bed.gz mm10 released mild to moderate bottlenecking, low read depth, control low read depth, inconsistent platforms, low read length, moderate library complexity ENCFF597MNA bed narrowPeak optimal idr thresholded peaks ENCSR000ERE ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MXI1-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF411DQD, ENCFF547MET, ENCFF774NDZ, ENCFF933KUS 607171 ENCODE Processing Pipeline eff9a7917a097096c3868fb1ba776295 https://www.encodeproject.org/files/ENCFF597MNA/@@download/ENCFF597MNA.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth ENCFF986QOL bed narrowPeak optimal idr thresholded peaks ENCSR000AIB ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus CEBPB-mouse DNA see document see document False 2011-11-23 ENCODE 1, 2 ENCFF042VSD, ENCFF255COK, ENCFF547MET, ENCFF980ZHP 276403 ENCODE Processing Pipeline 8cd66cd28d12f9821022575c15716172 https://www.encodeproject.org/files/ENCFF986QOL/@@download/ENCFF986QOL.bed.gz mm10 released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF903KGH bed narrowPeak optimal idr thresholded peaks ENCSR000CEG ChIP-seq UBERON:0000473 testis tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF198QXS, ENCFF547MET, ENCFF590QKD, ENCFF864LRN 348196 ENCODE Processing Pipeline 510c7f5bf5355ad4ed5e7dda3cca35b5 https://www.encodeproject.org/files/ENCFF903KGH/@@download/ENCFF903KGH.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms, low read depth control insufficient read depth ENCFF093MTA bed narrowPeak optimal idr thresholded peaks ENCSR000EQS ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus GABPA-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF384FWP, ENCFF547MET, ENCFF781YMH, ENCFF984MWK 41438 ENCODE Processing Pipeline a2c63956a67640d8a72b455b55ea7f4c https://www.encodeproject.org/files/ENCFF093MTA/@@download/ENCFF093MTA.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment, low read depth insufficient replicate concordance ENCFF357KNB bed narrowPeak optimal idr thresholded peaks ENCSR000CBN ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF197CSD, ENCFF547MET, ENCFF558UQC, ENCFF863QLD 529140 ENCODE Processing Pipeline 10b28a33ce515cb97751db98d2e24758 https://www.encodeproject.org/files/ENCFF357KNB/@@download/ENCFF357KNB.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, control low read depth, low read length, moderate library complexity insufficient read depth ENCFF637JIJ bed narrowPeak optimal idr thresholded peaks ENCSR000ESN ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CHD1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF133DYG, ENCFF195SXV, ENCFF263TBO, ENCFF547MET 233724 ENCODE Processing Pipeline 8546e40e938b6db51319cb4b7f2dcbc3 https://www.encodeproject.org/files/ENCFF637JIJ/@@download/ENCFF637JIJ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF443TPY bed narrowPeak optimal idr thresholded peaks ENCSR000CEF ChIP-seq UBERON:0000473 testis tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF334UXG, ENCFF502SKJ, ENCFF547MET, ENCFF901PPE 396257 ENCODE Processing Pipeline 632e5b2a4adf5b126946abb51f5ce210 https://www.encodeproject.org/files/ENCFF443TPY/@@download/ENCFF443TPY.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth control insufficient read depth, insufficient read depth, insufficient replicate concordance ENCFF130OBI bed narrowPeak optimal idr thresholded peaks ENCSR000ERN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MYC-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF160KXR, ENCFF434IOC, ENCFF547MET, ENCFF962BGJ 555360 ENCODE Processing Pipeline 4cdb840a799631505bd91fd35fb41252 https://www.encodeproject.org/files/ENCFF130OBI/@@download/ENCFF130OBI.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth ENCFF573INC bed narrowPeak optimal idr thresholded peaks ENCSR000EUA ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MYC-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF139JHS, ENCFF363WUG, ENCFF509VJZ, ENCFF547MET 521274 ENCODE Processing Pipeline 4dbf87184df644fcaccf4598ad735e97 https://www.encodeproject.org/files/ENCFF573INC/@@download/ENCFF573INC.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF567VSU bed narrowPeak optimal idr thresholded peaks ENCSR000ESI ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus RCOR1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF017UZY, ENCFF137KKN, ENCFF547MET, ENCFF701CYM 510153 ENCODE Processing Pipeline 39172ed0f47af19a093793e5bbd26c8c https://www.encodeproject.org/files/ENCFF567VSU/@@download/ENCFF567VSU.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF929RJU bed narrowPeak optimal idr thresholded peaks ENCSR000DIR ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF163MHO, ENCFF456FUK, ENCFF547MET, ENCFF638XCM 461703 ENCODE Processing Pipeline d668027fd0716f46246446025db4c677 https://www.encodeproject.org/files/ENCFF929RJU/@@download/ENCFF929RJU.bed.gz mm10 released mixed read lengths, low read length, inconsistent platforms, low read depth biological replicates with identical biosample insufficient read depth ENCFF676PFD bed narrowPeak optimal idr thresholded peaks ENCSR000ETG ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus dimethyl sulfoxide 2 percent 5 day POLR2A-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF490UJP, ENCFF547MET, ENCFF691FKN, ENCFF806WJV 660076 ENCODE Processing Pipeline a17122ab6e27dcfc43d3d2bd09d8f695 https://www.encodeproject.org/files/ENCFF676PFD/@@download/ENCFF676PFD.bed.gz mm10 released low read length, mild to moderate bottlenecking, moderate library complexity, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF034VZI bed narrowPeak optimal idr thresholded peaks ENCSR000CBO ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF068IFU, ENCFF234JEC, ENCFF513QUA, ENCFF547MET 517919 ENCODE Processing Pipeline 4dcd43bc5a2693cb77a89aacd5d174b0 https://www.encodeproject.org/files/ENCFF034VZI/@@download/ENCFF034VZI.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth insufficient read depth extremely low read depth ENCFF495VWK bed narrowPeak optimal idr thresholded peaks ENCSR000DIG ChIP-seq EFO:0002034 G1E stem cell Mus musculus POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF380TVB, ENCFF517GSF, ENCFF547MET, ENCFF835XEQ 61626 ENCODE Processing Pipeline 05cee7428b0ab274f03608505df72b30 https://www.encodeproject.org/files/ENCFF495VWK/@@download/ENCFF495VWK.bed.gz mm10 released low read length, inconsistent platforms, low read depth biological replicates with identical biosample insufficient replicate concordance ENCFF119XEH bed narrowPeak optimal idr thresholded peaks ENCSR000CEA ChIP-seq UBERON:0002370 thymus tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF284NSF, ENCFF487HJO, ENCFF521RKR, ENCFF547MET 234446 ENCODE Processing Pipeline e7134bd8cf4ac63d6347ffc764c60e1c https://www.encodeproject.org/files/ENCFF119XEH/@@download/ENCFF119XEH.bed.gz mm10 released low read length, mild to moderate bottlenecking, moderate library complexity, control low read depth insufficient read depth, poor library complexity, control insufficient read depth extremely low read depth ENCFF950CJS bed narrowPeak optimal idr thresholded peaks ENCSR000ETM ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF193ZKP, ENCFF212LAR, ENCFF541QIH, ENCFF547MET 382232 ENCODE Processing Pipeline 4365e229fa9904fa8d0b9c6812ea275c https://www.encodeproject.org/files/ENCFF950CJS/@@download/ENCFF950CJS.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF616HYA bed narrowPeak optimal idr thresholded peaks ENCSR000CBI ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF366XDH, ENCFF447SUY, ENCFF547MET, ENCFF644KRF 577078 ENCODE Processing Pipeline 460ef0f9b0836dd60f0c1212d21d83fa https://www.encodeproject.org/files/ENCFF616HYA/@@download/ENCFF616HYA.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth, mixed read lengths insufficient read depth, insufficient read length ENCFF383PSV bed narrowPeak optimal idr thresholded peaks ENCSR000CCA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF547MET, ENCFF578UCL, ENCFF765TKX, ENCFF851FMZ 603676 ENCODE Processing Pipeline f1fc071be9a60f59977f01dc87253610 https://www.encodeproject.org/files/ENCFF383PSV/@@download/ENCFF383PSV.bed.gz mm10 released low read length, control low read depth insufficient read depth ENCFF184NQJ bed narrowPeak optimal idr thresholded peaks ENCSR000EQP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZMIZ1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF547MET, ENCFF636ZRW, ENCFF860QAI, ENCFF931CZF 324673 ENCODE Processing Pipeline de8404d8fe9504773c93c66f6f2cebe0 https://www.encodeproject.org/files/ENCFF184NQJ/@@download/ENCFF184NQJ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF791EKG bed narrowPeak optimal idr thresholded peaks ENCSR000ETT ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus dimethyl sulfoxide 2 percent 5 day RAD21-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF547MET, ENCFF757HWH, ENCFF781DWI, ENCFF865CMY 510101 ENCODE Processing Pipeline b647d54fbffd121a72cd60c06deda226 https://www.encodeproject.org/files/ENCFF791EKG/@@download/ENCFF791EKG.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF347BWU bed narrowPeak optimal idr thresholded peaks ENCSR362VNF ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus CTCF-mouse DNA see document see document False 2014-02-24 ENCODE 1, 2 ENCFF100ZNH, ENCFF243PIS, ENCFF456EVZ, ENCFF547MET 713139 ENCODE Processing Pipeline be25fe80a8c1e6d77057eeffc0d7ec5f https://www.encodeproject.org/files/ENCFF347BWU/@@download/ENCFF347BWU.bed.gz mm10 released low read length experiment not submitted to GEO ENCFF228CPY bed narrowPeak optimal idr thresholded peaks ENCSR000ERL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAX-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF291AVC, ENCFF331PXR, ENCFF547MET, ENCFF802FDG 561836 ENCODE Processing Pipeline ddfb2d963406a72df84e7e836049202f https://www.encodeproject.org/files/ENCFF228CPY/@@download/ENCFF228CPY.bed.gz mm10 released low read length, inconsistent target of control experiment ENCFF956UZL bed narrowPeak optimal idr thresholded peaks ENCSR527DME ChIP-seq UBERON:0002048 lung tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1, 2 ENCFF165TDV, ENCFF485TBQ, ENCFF547MET, ENCFF718HWX 784401 ENCODE Processing Pipeline 75cc9a7fcfd6dd8e05485319aba618fa https://www.encodeproject.org/files/ENCFF956UZL/@@download/ENCFF956UZL.bed.gz mm10 released mild to moderate bottlenecking, control low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF179FJG bed narrowPeak optimal idr thresholded peaks ENCSR000CCD ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF397PQB, ENCFF547MET, ENCFF928UGN, ENCFF989VZZ 480846 ENCODE Processing Pipeline ae8242dd330ecff2c0a4f26afb24ccd6 https://www.encodeproject.org/files/ENCFF179FJG/@@download/ENCFF179FJG.bed.gz mm10 released low read length insufficient read depth ENCFF968IBZ bed narrowPeak optimal idr thresholded peaks ENCSR000ETW ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF2-mouse DNA see document see document False 2011-02-07 ENCODE 1, 2 ENCFF033VUP, ENCFF087TTA, ENCFF424HUK, ENCFF547MET 25948 ENCODE Processing Pipeline 6742802fe64e87a234954ab8df683d42 https://www.encodeproject.org/files/ENCFF968IBZ/@@download/ENCFF968IBZ.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample insufficient read depth ENCFF031DDU bed narrowPeak optimal idr thresholded peaks ENCSR000ETK ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAFK-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF506MCL, ENCFF512TDJ, ENCFF547MET, ENCFF579OLU 165979 ENCODE Processing Pipeline 3adb68a32b8636e7e784f238306daffd https://www.encodeproject.org/files/ENCFF031DDU/@@download/ENCFF031DDU.bed.gz mm10 released borderline replicate concordance, low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF700PEG bed narrowPeak optimal idr thresholded peaks ENCSR000EUB ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TBP-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF258ZVQ, ENCFF547MET, ENCFF862BHO, ENCFF884FLM 539838 ENCODE Processing Pipeline 9ce5e95026614e56564b749973555582 https://www.encodeproject.org/files/ENCFF700PEG/@@download/ENCFF700PEG.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF459OJI bed narrowPeak optimal idr thresholded peaks ENCSR000ERD ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NELFE-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF507OCS, ENCFF547MET, ENCFF850JWX, ENCFF915TKM 357561 ENCODE Processing Pipeline fa24b929d1a786ccbdf404690caad384 https://www.encodeproject.org/files/ENCFF459OJI/@@download/ENCFF459OJI.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF449MCJ bed narrowPeak optimal idr thresholded peaks ENCSR000EQX ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus UBTF-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF053QBJ, ENCFF405OWO, ENCFF547MET, ENCFF966DTT 229623 ENCODE Processing Pipeline fb23ef72a524a4628a6b0b69a366985d https://www.encodeproject.org/files/ENCFF449MCJ/@@download/ENCFF449MCJ.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity ENCFF941FDR bed narrowPeak optimal idr thresholded peaks ENCSR000ETV ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus EP300-mouse DNA see document see document False 2011-02-07 ENCODE 1, 2 ENCFF352UNG, ENCFF547MET, ENCFF582KWA, ENCFF665HJW 647297 ENCODE Processing Pipeline 8f2410cfb9221aeb53f8f5757315afbd https://www.encodeproject.org/files/ENCFF941FDR/@@download/ENCFF941FDR.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF345FTL bed narrowPeak optimal idr thresholded peaks ENCSR000ETR ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MYB-mouse DNA see document see document False 2011-02-07 ENCODE 1, 2 ENCFF075ENR, ENCFF547MET, ENCFF610JIV, ENCFF841UND 191722 ENCODE Processing Pipeline cf2b0536f1f8f619441e10fb32511465 https://www.encodeproject.org/files/ENCFF345FTL/@@download/ENCFF345FTL.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF116ZIX bed narrowPeak optimal idr thresholded peaks ENCSR418SBY ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF410PVV, ENCFF547MET, ENCFF707HGS, ENCFF985TTQ 1027357 ENCODE Processing Pipeline eda07a85a8016996d2daf94e04674906 https://www.encodeproject.org/files/ENCFF116ZIX/@@download/ENCFF116ZIX.bed.gz mm10 released antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF228IWF bed narrowPeak optimal idr thresholded peaks ENCSR000EUC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2A-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF547BST, ENCFF547MET, ENCFF659FDY, ENCFF736BXZ 555351 ENCODE Processing Pipeline c0f83d3803366ad5ff188031f7502e2c https://www.encodeproject.org/files/ENCFF228IWF/@@download/ENCFF228IWF.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF143RHK bed narrowPeak optimal idr thresholded peaks ENCSR000CDX ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF473UHO, ENCFF547MET, ENCFF825DDG, ENCFF910QVG 233522 ENCODE Processing Pipeline 8193beedd91a6a28ea77b25367df8d14 https://www.encodeproject.org/files/ENCFF143RHK/@@download/ENCFF143RHK.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, low read depth extremely low read depth ENCFF319LOC bed narrowPeak optimal idr thresholded peaks ENCSR000CED ChIP-seq UBERON:0002108 small intestine tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF023IJI, ENCFF547MET, ENCFF715VNT, ENCFF893SUP 486999 ENCODE Processing Pipeline eed84a0b1641898c5b088f213a844092 https://www.encodeproject.org/files/ENCFF319LOC/@@download/ENCFF319LOC.bed.gz mm10 released mild to moderate bottlenecking, mixed read lengths, low read depth, inconsistent platforms, control low read depth, low read length, moderate library complexity insufficient read length, insufficient replicate concordance extremely low read depth ENCFF724FOF bed narrowPeak optimal idr thresholded peaks ENCSR000DIQ ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF101JMH, ENCFF382TKE, ENCFF547MET, ENCFF684HMD 159070 ENCODE Processing Pipeline 9fb3cab31531732d0ac1c02ea36c46ea https://www.encodeproject.org/files/ENCFF724FOF/@@download/ENCFF724FOF.bed.gz mm10 released low read length, inconsistent platforms, mixed read lengths biological replicates with identical biosample ENCFF041IHJ bed narrowPeak optimal idr thresholded peaks ENCSR000CCC ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF356JZY, ENCFF547MET, ENCFF601PHQ, ENCFF899LLH 153885 ENCODE Processing Pipeline b92f3c2366b4b8b8419599a973f65253 https://www.encodeproject.org/files/ENCFF041IHJ/@@download/ENCFF041IHJ.bed.gz mm10 released low read length, borderline replicate concordance insufficient read depth ENCFF375GXQ bed narrowPeak optimal idr thresholded peaks ENCSR000ETP ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus EP300-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF246EZG, ENCFF304STF, ENCFF472IDT, ENCFF547MET 768067 ENCODE Processing Pipeline 9ba1154a14e969ac2d6f2c90cf2a5013 https://www.encodeproject.org/files/ENCFF375GXQ/@@download/ENCFF375GXQ.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF458BGT bed narrowPeak optimal idr thresholded peaks ENCSR194GNY ChIP-seq UBERON:0002107 liver tissue Mus musculus GATA4-mouse DNA see document see document False 2014-03-14 ENCODE 1, 2 ENCFF034VDK, ENCFF436NIK, ENCFF547MET, ENCFF762AWW 414781 ENCODE Processing Pipeline 90b68db67e07d20a12671ce2763be882 https://www.encodeproject.org/files/ENCFF458BGT/@@download/ENCFF458BGT.bed.gz mm10 released low read length, mild to moderate bottlenecking experiment not submitted to GEO, biological replicates with identical biosample insufficient replicate concordance ENCFF486IVR bed narrowPeak optimal idr thresholded peaks ENCSR000ERU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus E2F4-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF099HHW, ENCFF211VZG, ENCFF547MET, ENCFF632ZQE 120469 ENCODE Processing Pipeline 8686434c9474ab0865f3270ca2e2c2b5 https://www.encodeproject.org/files/ENCFF486IVR/@@download/ENCFF486IVR.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth insufficient replicate concordance ENCFF399UKJ bed narrowPeak optimal idr thresholded peaks ENCSR000ETO ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CHD2-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF026ZEY, ENCFF383VAH, ENCFF547MET, ENCFF574WAP 105687 ENCODE Processing Pipeline c9d418cd74f7e615293b4e65566197f1 https://www.encodeproject.org/files/ENCFF399UKJ/@@download/ENCFF399UKJ.bed.gz mm10 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF618DXI bed narrowPeak optimal idr thresholded peaks ENCSR677SIH ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1, 2 ENCFF040OPZ, ENCFF095TOF, ENCFF452VPT, ENCFF547MET 886626 ENCODE Processing Pipeline fd91f0be18f3e41b463bbde7375a0198 https://www.encodeproject.org/files/ENCFF618DXI/@@download/ENCFF618DXI.bed.gz mm10 released antibody characterized with exemption, low read depth NTR biosample, biological replicates with identical biosample ENCFF965MMO bed narrowPeak optimal idr thresholded peaks ENCSR000ERP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TBP-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF037DYV, ENCFF480KIU, ENCFF547MET, ENCFF944CTC 414158 ENCODE Processing Pipeline f6eb7b5bd474f94cde2c65c4b5ca49f0 https://www.encodeproject.org/files/ENCFF965MMO/@@download/ENCFF965MMO.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF605YVN bed narrowPeak optimal idr thresholded peaks ENCSR000CBV ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF367LMD, ENCFF547MET, ENCFF678KWQ, ENCFF967TRS 488435 ENCODE Processing Pipeline 2425e89fc649dea77d09fe3ed033bd3e https://www.encodeproject.org/files/ENCFF605YVN/@@download/ENCFF605YVN.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth insufficient read depth ENCFF162EBI bed narrowPeak optimal idr thresholded peaks ENCSR000DIL ChIP-seq CL:0000765 erythroblast primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF188TYP, ENCFF337HVO, ENCFF540LXX, ENCFF547MET 138232 ENCODE Processing Pipeline b87d70d97d4c620ea0c896ebc17a62a0 https://www.encodeproject.org/files/ENCFF162EBI/@@download/ENCFF162EBI.bed.gz mm10 released low read length, inconsistent platforms, mixed read lengths ENCFF255MHA bed narrowPeak optimal idr thresholded peaks ENCSR000ERV ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF338BOV, ENCFF456SWU, ENCFF547MET, ENCFF869DLF 419921 ENCODE Processing Pipeline 5134699728e120b67018ddd72f2ad547 https://www.encodeproject.org/files/ENCFF255MHA/@@download/ENCFF255MHA.bed.gz mm10 released low read length, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF119CZQ bed narrowPeak optimal idr thresholded peaks ENCSR000ETL ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus SMC3-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF029XTX, ENCFF325YXC, ENCFF547MET, ENCFF952MLM 676618 ENCODE Processing Pipeline 58a5d8389217a038e385c251d6a59ae9 https://www.encodeproject.org/files/ENCFF119CZQ/@@download/ENCFF119CZQ.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF780JWE bed narrowPeak optimal idr thresholded peaks ENCSR000ERH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF048NGW, ENCFF250LEC, ENCFF351DDA, ENCFF547MET 277110 ENCODE Processing Pipeline c68043cc17f592eca0ec0a6e3aab0f47 https://www.encodeproject.org/files/ENCFF780JWE/@@download/ENCFF780JWE.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF451ZPC bed narrowPeak optimal idr thresholded peaks ENCSR000ETA ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus dimethyl sulfoxide 2 percent 5 day GATA1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF170CUA, ENCFF332WUR, ENCFF439TUB, ENCFF547MET 457750 ENCODE Processing Pipeline 6afe57353c674fc5ee94857647777768 https://www.encodeproject.org/files/ENCFF451ZPC/@@download/ENCFF451ZPC.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth biological replicates with identical biosample ENCFF847VTQ bed narrowPeak optimal idr thresholded peaks ENCSR000ETF ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF2-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF140WUQ, ENCFF274IPR, ENCFF448VYN, ENCFF547MET 79371 ENCODE Processing Pipeline 97de8795100b982fe1acaabf1b74f139 https://www.encodeproject.org/files/ENCFF847VTQ/@@download/ENCFF847VTQ.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF495GBW bed narrowPeak optimal idr thresholded peaks ENCSR779CZG ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus NANOG-mouse DNA see document see document False 2014-03-14 ENCODE 1, 2 ENCFF478BIW, ENCFF547MET, ENCFF717OFI, ENCFF752WKJ 287900 ENCODE Processing Pipeline 0ae8fa52a3e0d20810077c120a7ebd25 https://www.encodeproject.org/files/ENCFF495GBW/@@download/ENCFF495GBW.bed.gz mm10 released mixed read lengths, low read length, borderline replicate concordance experiment not submitted to GEO ENCFF589AAH bed narrowPeak optimal idr thresholded peaks ENCSR000ETZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus JUND-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF053BUD, ENCFF186EFZ, ENCFF547MET, ENCFF900VBP 135761 ENCODE Processing Pipeline c64ddd8c3be9e1c1649a1807c4547365 https://www.encodeproject.org/files/ENCFF589AAH/@@download/ENCFF589AAH.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF987ZSZ bed narrowPeak optimal idr thresholded peaks ENCSR705HGT ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF156OSF, ENCFF364BAN, ENCFF547MET, ENCFF569LXK 324326 ENCODE Processing Pipeline a48391f80ec9ed24eb322566535fedab https://www.encodeproject.org/files/ENCFF987ZSZ/@@download/ENCFF987ZSZ.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity experiment not submitted to GEO, biological replicates with identical biosample ENCFF874KZS bed narrowPeak optimal idr thresholded peaks ENCSR000CFK ChIP-seq CL:0002476 bone marrow macrophage primary cell Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF105OGD, ENCFF547MET, ENCFF593FDX, ENCFF705BHR 67370 ENCODE Processing Pipeline 2fb03acd7c9db55b8f7525ceb9ffca4b https://www.encodeproject.org/files/ENCFF874KZS/@@download/ENCFF874KZS.bed.gz mm10 released borderline replicate concordance, low read length, mild to moderate bottlenecking, low read depth ENCFF683MGY bed narrowPeak optimal idr thresholded peaks ENCSR293WTN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF393SFN, ENCFF547MET, ENCFF610OEV, ENCFF890ZJF 524918 ENCODE Processing Pipeline afd5e5b8f706016c408592beba12e6ab https://www.encodeproject.org/files/ENCFF683MGY/@@download/ENCFF683MGY.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth experiment not submitted to GEO ENCFF219OVU bed narrowPeak optimal idr thresholded peaks ENCSR000EUG ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus GATA1-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF041ZRE, ENCFF153NNX, ENCFF282VZU, ENCFF547MET 792922 ENCODE Processing Pipeline 6c2a10fa95692479bbb15cd0d0736a96 https://www.encodeproject.org/files/ENCFF219OVU/@@download/ENCFF219OVU.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth biological replicates with identical biosample ENCFF128TGM bed narrowPeak optimal idr thresholded peaks ENCSR000EQY ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SIN3A-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF221YDR, ENCFF488GVO, ENCFF547MET, ENCFF943ETE 701782 ENCODE Processing Pipeline 72d81a98572e04580758a41d0bc06113 https://www.encodeproject.org/files/ENCFF128TGM/@@download/ENCFF128TGM.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment ENCFF353DJA bed narrowPeak optimal idr thresholded peaks ENCSR973SOG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF285ZBQ, ENCFF301YAS, ENCFF547MET, ENCFF994TGI 146661 ENCODE Processing Pipeline a6e07c6f4faf7b8e3a9d8c28972946c7 https://www.encodeproject.org/files/ENCFF353DJA/@@download/ENCFF353DJA.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth experiment not submitted to GEO ENCFF551TDS bed narrowPeak optimal idr thresholded peaks ENCSR349JDH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF547MET, ENCFF619BMP, ENCFF705OQG, ENCFF881QFU 684063 ENCODE Processing Pipeline 2ab1c017e0ed3cf2f7be3af7f0515869 https://www.encodeproject.org/files/ENCFF551TDS/@@download/ENCFF551TDS.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity experiment not submitted to GEO, biological replicates with identical biosample ENCFF554BKP bed narrowPeak optimal idr thresholded peaks ENCSR743ZJL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus IRF4-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF291UJL, ENCFF547MET, ENCFF856YRM, ENCFF946OOG 791132 ENCODE Processing Pipeline 895d8851b97a3a9fe6b8eb4cdf45e543 https://www.encodeproject.org/files/ENCFF554BKP/@@download/ENCFF554BKP.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth experiment not submitted to GEO ENCFF333ULW bed narrowPeak optimal idr thresholded peaks ENCSR000DIH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus PAX5-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF346ZZZ, ENCFF449JJN, ENCFF547MET, ENCFF698CKE 3479 ENCODE Processing Pipeline 5ab0e8fea84a982a46894a0495783cc6 https://www.encodeproject.org/files/ENCFF333ULW/@@download/ENCFF333ULW.bed.gz mm10 released low read length, inconsistent platforms, mixed read lengths ENCFF788VGC bed narrowPeak optimal idr thresholded peaks ENCSR000CBQ ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF084NYP, ENCFF161DMN, ENCFF245CWG, ENCFF547MET 325999 ENCODE Processing Pipeline 63a89f00daa1e6e86535addd162cff41 https://www.encodeproject.org/files/ENCFF788VGC/@@download/ENCFF788VGC.bed.gz mm10 released low read length, control low read depth, borderline replicate concordance insufficient read depth ENCFF988EWY bed narrowPeak optimal idr thresholded peaks ENCSR000CBT ChIP-seq UBERON:0002048 lung tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF460DBD, ENCFF547MET, ENCFF752OXC, ENCFF938KPF 364466 ENCODE Processing Pipeline 116363c42358bf65b2d8d4f5632a329b https://www.encodeproject.org/files/ENCFF988EWY/@@download/ENCFF988EWY.bed.gz mm10 released borderline replicate concordance, low read length, mild to moderate bottlenecking, control low read depth, low read depth extremely low read depth ENCFF530THK bed narrowPeak optimal idr thresholded peaks ENCSR000ERA ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ETS1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF268GPJ, ENCFF547MET, ENCFF821HYG, ENCFF916JGK 558681 ENCODE Processing Pipeline 1428adaf1485bbb84bc3895dd2853055 https://www.encodeproject.org/files/ENCFF530THK/@@download/ENCFF530THK.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity ENCFF599GJE bed narrowPeak optimal idr thresholded peaks ENCSR604XDL ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus MAFK-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF111KNX, ENCFF254FAR, ENCFF331PWC, ENCFF547MET 300989 ENCODE Processing Pipeline 475b6cd9a23895688adf1c714694bf7b https://www.encodeproject.org/files/ENCFF599GJE/@@download/ENCFF599GJE.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth ENCFF647NWK bed narrowPeak optimal idr thresholded peaks ENCSR000CBP ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF287OUE, ENCFF547MET, ENCFF597EPU, ENCFF631EVW 330458 ENCODE Processing Pipeline 56a7e6ff11120dc6c5b99c2fd92932b7 https://www.encodeproject.org/files/ENCFF647NWK/@@download/ENCFF647NWK.bed.gz mm10 released low read length, mild to moderate bottlenecking, control low read depth insufficient read depth extremely low read depth ENCFF716KJE bed narrowPeak optimal idr thresholded peaks ENCSR000ETX ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAX-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF145IUH, ENCFF289XJE, ENCFF324WCV, ENCFF547MET 525778 ENCODE Processing Pipeline 4a9a31c17efae46e029d29a6f46f9a09 https://www.encodeproject.org/files/ENCFF716KJE/@@download/ENCFF716KJE.bed.gz mm10 released low read length, inconsistent target of control experiment biological replicates with identical biosample ENCFF613TDJ bed narrowPeak optimal idr thresholded peaks ENCSR980YXJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF018QPL, ENCFF434PTP, ENCFF482CYN, ENCFF547MET 316860 ENCODE Processing Pipeline 8c33551da2197b0e4c668864addca82b https://www.encodeproject.org/files/ENCFF613TDJ/@@download/ENCFF613TDJ.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity experiment not submitted to GEO ENCFF766ABJ bed narrowPeak optimal idr thresholded peaks ENCSR000ERJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF2-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF101GGW, ENCFF213QTT, ENCFF547MET, ENCFF876DTD 103085 ENCODE Processing Pipeline e417de34d2464f750ce181ea0eaebf0e https://www.encodeproject.org/files/ENCFF766ABJ/@@download/ENCFF766ABJ.bed.gz mm10 released low read length, inconsistent target of control experiment, low read depth ENCFF625UEM bed narrowPeak optimal idr thresholded peaks ENCSR000ESG ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF323ECU, ENCFF547MET, ENCFF793LKL, ENCFF882JUL 451440 ENCODE Processing Pipeline f1a3a535f1a1fec18eeda82f3f3d64e5 https://www.encodeproject.org/files/ENCFF625UEM/@@download/ENCFF625UEM.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample ENCFF253NHY bed narrowPeak optimal idr thresholded peaks ENCSR000CFJ ChIP-seq CL:0002476 bone marrow macrophage primary cell Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1, 2 ENCFF330SNH, ENCFF547MET, ENCFF738VPY, ENCFF755GYG 343598 ENCODE Processing Pipeline d60a0cbb723d353c09886c8e13308594 https://www.encodeproject.org/files/ENCFF253NHY/@@download/ENCFF253NHY.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, low read depth ENCFF044OUI bed narrowPeak optimal idr thresholded peaks ENCSR867SDZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF425HUT, ENCFF547MET, ENCFF571RCH, ENCFF613LTH 94709 ENCODE Processing Pipeline 33636b3a6a1e97a8984d21e425ab3f53 https://www.encodeproject.org/files/ENCFF044OUI/@@download/ENCFF044OUI.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth experiment not submitted to GEO, biological replicates with identical biosample severe bottlenecking, poor library complexity, insufficient replicate concordance extremely low read depth ENCFF443MGH bed narrowPeak optimal idr thresholded peaks ENCSR135SWH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF150DQT, ENCFF327ALQ, ENCFF547MET, ENCFF958NPV 200903 ENCODE Processing Pipeline 45883363b308683581b848b51f76a685 https://www.encodeproject.org/files/ENCFF443MGH/@@download/ENCFF443MGH.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF885EHG bed narrowPeak optimal idr thresholded peaks ENCSR033OWC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF130MWN, ENCFF547MET, ENCFF746CPX, ENCFF838NPZ 363539 ENCODE Processing Pipeline 92906234a7c7b9e6aebbd9246ec1b6bd https://www.encodeproject.org/files/ENCFF885EHG/@@download/ENCFF885EHG.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity experiment not submitted to GEO, biological replicates with identical biosample ENCFF561HFB bed narrowPeak optimal idr thresholded peaks ENCSR000EQO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF441NPO, ENCFF547MET, ENCFF572NST, ENCFF646FIZ 554771 ENCODE Processing Pipeline b74cebaea8173499b5e08c84a42c358e https://www.encodeproject.org/files/ENCFF561HFB/@@download/ENCFF561HFB.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF066CEV bed narrowPeak optimal idr thresholded peaks ENCSR000ESX ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZKSCAN1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF014SUM, ENCFF470PMX, ENCFF547MET, ENCFF745JTK 85661 ENCODE Processing Pipeline 369dc9b71be1b62101d7682e26dc451c https://www.encodeproject.org/files/ENCFF066CEV/@@download/ENCFF066CEV.bed.gz mm10 released mild to moderate bottlenecking, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment, moderate library complexity biological replicates with identical biosample ENCFF072JMS bed narrowPeak optimal idr thresholded peaks ENCSR000EQR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF388WVI, ENCFF547MET, ENCFF710VPX, ENCFF984NJU 401037 ENCODE Processing Pipeline a49088963d6e8e4c4e243c445c63e8fc https://www.encodeproject.org/files/ENCFF072JMS/@@download/ENCFF072JMS.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF079ITK bed narrowPeak optimal idr thresholded peaks ENCSR906QEK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF450XHA, ENCFF547MET, ENCFF782LDU, ENCFF885IKN 648800 ENCODE Processing Pipeline a538df273a2b23d31a164ba1c571f817 https://www.encodeproject.org/files/ENCFF079ITK/@@download/ENCFF079ITK.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, inconsistent target of control experiment, low read depth experiment not submitted to GEO ENCFF468PLO bed narrowPeak optimal idr thresholded peaks ENCSR000ETC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus SIN3A-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF335JBI, ENCFF547MET, ENCFF566TGG, ENCFF780EPD 916833 ENCODE Processing Pipeline 466cad4e469c800c404aa6d99fe6a11d https://www.encodeproject.org/files/ENCFF468PLO/@@download/ENCFF468PLO.bed.gz mm10 released low read length, inconsistent platforms, inconsistent target of control experiment biological replicates with identical biosample ENCFF981ENW bed narrowPeak optimal idr thresholded peaks ENCSR000ESH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus BHLHE40-mouse DNA see document see document False 2012-08-16 ENCODE 1, 2 ENCFF363EXK, ENCFF494YES, ENCFF547MET, ENCFF561ZYK 312995 ENCODE Processing Pipeline 0ea0e673f1b8c32f2a837e8b4d37e448 https://www.encodeproject.org/files/ENCFF981ENW/@@download/ENCFF981ENW.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment duplicate lane review, biological replicates with identical biosample ENCFF612GBQ bed narrowPeak optimal idr thresholded peaks ENCSR000ERO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUN-mouse DNA see document see document False 2011-09-19 ENCODE 1, 2 ENCFF379UVJ, ENCFF525UBB, ENCFF547MET, ENCFF999AHU 219439 ENCODE Processing Pipeline 7969d02e58f8bed5f6fe8bf47dc5db20 https://www.encodeproject.org/files/ENCFF612GBQ/@@download/ENCFF612GBQ.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, inconsistent target of control experiment, low read depth insufficient read depth ENCFF373CDN bed narrowPeak optimal idr thresholded peaks ENCSR531HWD ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus CHD2-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF098AAD, ENCFF192FJH, ENCFF410WXS, ENCFF547MET 154253 ENCODE Processing Pipeline 699e3b424c443869f1f5158abbc4f39d https://www.encodeproject.org/files/ENCFF373CDN/@@download/ENCFF373CDN.bed.gz mm10 released low read length, mild to moderate bottlenecking, inconsistent platforms, low read depth experiment not submitted to GEO, biological replicates with identical biosample ENCFF062DPL bed narrowPeak optimal idr thresholded peaks ENCSR806JZK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 1, 2 ENCFF498DFC, ENCFF547MET, ENCFF596FSM, ENCFF704GUT 573775 ENCODE Processing Pipeline 140af3c0c17233516d059ea23a421922 https://www.encodeproject.org/files/ENCFF062DPL/@@download/ENCFF062DPL.bed.gz mm10 released mild to moderate bottlenecking, borderline replicate concordance, low read depth, inconsistent platforms, low read length, inconsistent target of control experiment experiment not submitted to GEO ENCFF100YLI bed narrowPeak optimal idr thresholded peaks ENCSR000CBW ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1, 2 ENCFF507FHH, ENCFF508GAH, ENCFF547MET, ENCFF929APL 345379 ENCODE Processing Pipeline 20bcde137a04241c61036572d6657bf7 https://www.encodeproject.org/files/ENCFF100YLI/@@download/ENCFF100YLI.bed.gz mm10 released low read length, moderate library complexity, mild to moderate bottlenecking, control low read depth, borderline replicate concordance insufficient read depth ENCFF501HSN bed narrowPeak optimal idr thresholded peaks ENCSR000EQW ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZKSCAN1-mouse DNA see document see document False 2012-06-15 ENCODE 1, 2 ENCFF077OGZ, ENCFF270QCB, ENCFF474CML, ENCFF547MET 44991 ENCODE Processing Pipeline 01b18e76103506fd84182c77d437cbfa https://www.encodeproject.org/files/ENCFF501HSN/@@download/ENCFF501HSN.bed.gz mm10 released borderline replicate concordance, low read length, inconsistent platforms, inconsistent target of control experiment, low read depth ENCFF332ZVZ bed narrowPeak optimal idr thresholded peaks ENCSR000DIE ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA2-mouse DNA see document see document False 2012-02-13 ENCODE 1, 2 ENCFF126SBW, ENCFF447ABB, ENCFF547MET, ENCFF840EKX 10843 ENCODE Processing Pipeline 2146de6de4c8fabcba289bdd928de53c https://www.encodeproject.org/files/ENCFF332ZVZ/@@download/ENCFF332ZVZ.bed.gz mm10 released borderline replicate concordance, low read length, inconsistent platforms, low read depth biological replicates with identical biosample