ENCFF002ADK fastq reads ENCSR194GNY ChIP-seq UBERON:0002107 liver tissue Mus musculus GATA4-mouse DNA see document see document False 2014-03-14 ENCODE 1 1 48 single-ended 1994901181 Ross Hardison, PennState 913ad45f406193014a6ce41fbf87c51f https://www.encodeproject.org/files/ENCFF002ADK/@@download/ENCFF002ADK.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZYW/ released low read length, mild to moderate bottlenecking experiment not submitted to GEO, biological replicates with identical biosample insufficient replicate concordance ENCFF002ADM fastq reads ENCSR194GNY ChIP-seq UBERON:0002107 liver tissue Mus musculus GATA4-mouse DNA see document see document False 2014-03-14 ENCODE 2 1 48 single-ended 1982912528 Ross Hardison, PennState a67834f4970f6c561be75aa305c2c135 https://www.encodeproject.org/files/ENCFF002ADM/@@download/ENCFF002ADM.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZYX/ released low read length, mild to moderate bottlenecking experiment not submitted to GEO, biological replicates with identical biosample insufficient replicate concordance ENCFF001IIF fastq reads ENCSR000AIW ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1062591253 Barbara Wold, Caltech 681bb4497c4540d61d1274829f3ace0a https://www.encodeproject.org/files/ENCFF001IIF/@@download/ENCFF001IIF.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released low read depth ENCFF001IIZ fastq reads ENCSR000AIE ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus USF1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1316268966 Barbara Wold, Caltech a70ed949cc8dacb54ebf6cf051a40d2f https://www.encodeproject.org/files/ENCFF001IIZ/@@download/ENCFF001IIZ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001LIY fastq reads ENCSR000CCB ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 748161937 Bing Ren, UCSD 395a8989661e9371c76790b9df3fede5 https://www.encodeproject.org/files/ENCFF001LIY/@@download/ENCFF001LIY.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KEU/ released low read length insufficient read depth ENCFF001MTY fastq reads ENCSR000DHD ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus FLI1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 55 single-ended 4215419263 Ross Hardison, PennState b5dee4a8a9ab7d8f26c8239cf03658c9 https://www.encodeproject.org/files/ENCFF001MTY/@@download/ENCFF001MTY.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUT/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms NTR biosample, biological replicates with identical biosample ENCFF001MTZ fastq reads ENCSR000DHD ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus FLI1-mouse DNA see document see document False 2012-08-07 ENCODE 2 1 48 single-ended 5159708324 Ross Hardison, PennState be60f748feb5eb302a40c7d9df58e816 https://www.encodeproject.org/files/ENCFF001MTZ/@@download/ENCFF001MTZ.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms NTR biosample, biological replicates with identical biosample ENCFF001MPN fastq reads ENCSR000DIN ChIP-seq EFO:0002034 G1E stem cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 36 single-ended 569247428 Ross Hardison, PennState ae7b53f47a2b2820ef60d3f3bd861f13 https://www.encodeproject.org/files/ENCFF001MPN/@@download/ENCFF001MPN.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MOR/ released low read length, low read depth, mixed read lengths, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001MPP fastq reads ENCSR000DIN ChIP-seq EFO:0002034 G1E stem cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 41 single-ended 854143018 Ross Hardison, PennState c0812f961ec1c6fcc58818a990421be3 https://www.encodeproject.org/files/ENCFF001MPP/@@download/ENCFF001MPP.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MPG/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001IHN fastq reads ENCSR000AIG ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 362051903 Barbara Wold, Caltech 4ec82286ec83cb00d075233992da259c https://www.encodeproject.org/files/ENCFF001IHN/@@download/ENCFF001IHN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released low read depth insufficient read length ENCFF001IHO fastq reads ENCSR000AIG ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 546755018 Barbara Wold, Caltech 6e545329c27a063f054f5fafa23ddc4b https://www.encodeproject.org/files/ENCFF001IHO/@@download/ENCFF001IHO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released low read depth insufficient read length ENCFF001IHP fastq reads ENCSR000AIG ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 559717731 Barbara Wold, Caltech 9da3908e4581c67589e4bf04312482ef https://www.encodeproject.org/files/ENCFF001IHP/@@download/ENCFF001IHP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released low read depth insufficient read length ENCFF001IHT fastq reads ENCSR000AIO ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MAX-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1584941463 Barbara Wold, Caltech 27e0edbf2b3e1b202e43cf5d2705a053 https://www.encodeproject.org/files/ENCFF001IHT/@@download/ENCFF001IHT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IFD/ released mild to moderate bottlenecking ENCFF001IDP fastq reads ENCSR000AIV ChIP-seq EFO:0001098 C2C12 cell line Mus musculus CEBPB-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1583392127 Barbara Wold, Caltech 3829991ad29d3f3696d3407fdf9c8833 https://www.encodeproject.org/files/ENCFF001IDP/@@download/ENCFF001IDP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IFD/ released low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001IFN fastq reads ENCSR000AIS ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus REST-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 1088968509 Barbara Wold, Caltech e7b97cb8edca3e8f4d9ee5d5205f6ca7 https://www.encodeproject.org/files/ENCFF001IFN/@@download/ENCFF001IFN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released mild to moderate bottlenecking, moderate library complexity insufficient read depth, insufficient read length ENCFF001IFO fastq reads ENCSR000AIS ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus REST-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 331435284 Barbara Wold, Caltech 0f9a9c343aed123dd0108f919859cf48 https://www.encodeproject.org/files/ENCFF001IFO/@@download/ENCFF001IFO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released mild to moderate bottlenecking, moderate library complexity insufficient read depth, insufficient read length ENCFF001IEL fastq reads ENCSR000AIK ChIP-seq EFO:0001098 C2C12 cell line Mus musculus FOSL1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 36 single-ended 924713947 Barbara Wold, Caltech 123a1f5c44fe1641162f67ae54da87c1 https://www.encodeproject.org/files/ENCFF001IEL/@@download/ENCFF001IEL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IFD/ released low read length, mild to moderate bottlenecking, inconsistent control read length, moderate library complexity insufficient read depth ENCFF001MPX fastq reads ENCSR000DHB ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 14 hour GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 55 single-ended 2676872071 Ross Hardison, PennState fc2b4c358006823c419c9f12dc20fc08 https://www.encodeproject.org/files/ENCFF001MPX/@@download/ENCFF001MPX.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MQW/ released mild to moderate bottlenecking, inconsistent control read length ENCFF001LTR fastq reads ENCSR000CEI ChIP-seq UBERON:0000955 brain tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 30 single-ended 178693182 Bing Ren, UCSD e31c12d864929dc493483dc7c6f688de https://www.encodeproject.org/files/ENCFF001LTR/@@download/ENCFF001LTR.fastq.gz Illumina Genome Analyzer II /files/ENCFF786ODW/ released mild to moderate bottlenecking, inconsistent control read length, inconsistent platforms severe bottlenecking, poor library complexity, insufficient read length extremely low read depth ENCFF001LTX fastq reads ENCSR000CEI ChIP-seq UBERON:0000955 brain tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 30 single-ended 999605431 Bing Ren, UCSD a997b11a58c8a7116f3b13569159b463 https://www.encodeproject.org/files/ENCFF001LTX/@@download/ENCFF001LTX.fastq.gz Illumina HiSeq 2000 /files/ENCFF001LAO/ released mild to moderate bottlenecking, inconsistent platforms severe bottlenecking, poor library complexity, insufficient read length extremely low read depth ENCFF001MVC fastq reads ENCSR000DHE ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 41 single-ended 629059358 Ross Hardison, PennState 9101d7b287d08b91fe7a2914cc9246da https://www.encodeproject.org/files/ENCFF001MVC/@@download/ENCFF001MVC.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MUT/ released low read length, low read depth, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MVJ fastq reads ENCSR000DHE ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-08-07 ENCODE 4 1 45 single-ended 2422864865 Ross Hardison, PennState 66c20c812b50f1bdca3489b48df92c50 https://www.encodeproject.org/files/ENCFF001MVJ/@@download/ENCFF001MVJ.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample ENCFF001MVL fastq reads ENCSR000DHE ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-08-07 ENCODE 2 1 55 single-ended 5721553125 Ross Hardison, PennState 90922c1d48a6749802f792f35a42a2b3 https://www.encodeproject.org/files/ENCFF001MVL/@@download/ENCFF001MVL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, low read depth, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MVN fastq reads ENCSR000DHE ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-08-07 ENCODE 3 1 48 single-ended 6252887485 Ross Hardison, PennState f3cf3f69dab547acfe0b4632f1b207d6 https://www.encodeproject.org/files/ENCFF001MVN/@@download/ENCFF001MVN.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample ENCFF001OBF fastq reads 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 1 36 single-ended 1088099293 Michael Snyder, Stanford 19d8aea39e93d119e68090a7c5c34fb7 https://www.encodeproject.org/files/ENCFF001OBF/@@download/ENCFF001OBF.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OBH fastq reads ENCSR000ESX ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZKSCAN1-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 880089580 Michael Snyder, Stanford 64a3973a2631d2d9e7788ebf2778bff5 https://www.encodeproject.org/files/ENCFF001OBH/@@download/ENCFF001OBH.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF205UPE fastq reads ENCSR135SWH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 652701041 Michael Snyder, Stanford cf7d157dcf2af337659f344f720e902a https://www.encodeproject.org/files/ENCFF205UPE/@@download/ENCFF205UPE.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF845NFO fastq reads ENCSR135SWH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 838164483 Michael Snyder, Stanford 8ca8d42db252c9c2ee8c49b402a0bd59 https://www.encodeproject.org/files/ENCFF845NFO/@@download/ENCFF845NFO.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF001NWM fastq reads ENCSR000ETN ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MXI1-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1010181748 Michael Snyder, Stanford 216a85454f84e59602c8b8fda8f1a9d6 https://www.encodeproject.org/files/ENCFF001NWM/@@download/ENCFF001NWM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NWN fastq reads 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 1 36 single-ended 1178409479 Michael Snyder, Stanford f48252e5837f1a4326c431586f48ea3e https://www.encodeproject.org/files/ENCFF001NWN/@@download/ENCFF001NWN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF443PSH fastq reads ENCSR806JZK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 674211387 Michael Snyder, Stanford 647e898a97f962f7011fa0cbaffcfac8 https://www.encodeproject.org/files/ENCFF443PSH/@@download/ENCFF443PSH.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms experiment not submitted to GEO ENCFF319ABF fastq reads ENCSR806JZK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 834889750 Michael Snyder, Stanford b5445b379112081796497099f3836cce https://www.encodeproject.org/files/ENCFF319ABF/@@download/ENCFF319ABF.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms experiment not submitted to GEO ENCFF001NGR fastq reads ENCSR000ERA ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ETS1-mouse DNA see document see document False 2012-06-15 ENCODE 1 1 36 single-ended 913008208 Michael Snyder, Stanford e0234974ff4469a0b05b8439a9921721 https://www.encodeproject.org/files/ENCFF001NGR/@@download/ENCFF001NGR.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001NGT fastq reads ENCSR000ERA ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ETS1-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 1042836880 Michael Snyder, Stanford 008aa46cbfb7b9b3ab6219f224cbd100 https://www.encodeproject.org/files/ENCFF001NGT/@@download/ENCFF001NGT.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001MVS fastq reads 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 1 36 single-ended 720724742 Ross Hardison, PennState c0c827d51cbd8179ee9e54c090f1f20f https://www.encodeproject.org/files/ENCFF001MVS/@@download/ENCFF001MVS.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MWB/ released low read length, low read depth, mixed read lengths, inconsistent platforms ENCFF001MVY fastq reads ENCSR000DIP ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 41 single-ended 1454271908 Ross Hardison, PennState 12a2d5932444ee5c3196b5038db710d8 https://www.encodeproject.org/files/ENCFF001MVY/@@download/ENCFF001MVY.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MWM/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms ENCFF001IGB fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 271153228 Barbara Wold, Caltech bf031200417f64458ab0600f2182e41e https://www.encodeproject.org/files/ENCFF001IGB/@@download/ENCFF001IGB.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF001IGC fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 206524109 Barbara Wold, Caltech 8705ce15b2072a5c057d105c34720458 https://www.encodeproject.org/files/ENCFF001IGC/@@download/ENCFF001IGC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF001IGD fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 358558672 Barbara Wold, Caltech 83b2b7a183a883dcb89dafa03233b287 https://www.encodeproject.org/files/ENCFF001IGD/@@download/ENCFF001IGD.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF001IGE fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 373146875 Barbara Wold, Caltech ad49c5a1c71670c001b78cb469fad61c https://www.encodeproject.org/files/ENCFF001IGE/@@download/ENCFF001IGE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF001IGG fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 286038108 Barbara Wold, Caltech 3b8dd0d8a1b4b065d24e762fa811fadd https://www.encodeproject.org/files/ENCFF001IGG/@@download/ENCFF001IGG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF001IGH fastq reads ENCSR000AID ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 274651076 Barbara Wold, Caltech 18d59f242692672abf157f74249cb7ff https://www.encodeproject.org/files/ENCFF001IGH/@@download/ENCFF001IGH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released mild to moderate bottlenecking insufficient read depth, insufficient read length ENCFF002ADY fastq reads ENCSR779CZG ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus NANOG-mouse DNA see document see document False 2014-03-14 ENCODE 1 1 45 single-ended 1634939989 Ross Hardison, PennState ada7126f8ff5fb2d97567d08190910f4 https://www.encodeproject.org/files/ENCFF002ADY/@@download/ENCFF002ADY.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGK/ released low read length, mixed read lengths, borderline replicate concordance experiment not submitted to GEO ENCFF002AEA fastq reads ENCSR779CZG ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus NANOG-mouse DNA see document see document False 2014-03-14 ENCODE 2 1 48 single-ended 1584558798 Ross Hardison, PennState 2a5a3f06b9b3d131b9ac7d0324d1247e https://www.encodeproject.org/files/ENCFF002AEA/@@download/ENCFF002AEA.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGM/ released low read length, mixed read lengths, inconsistent control read length, borderline replicate concordance experiment not submitted to GEO ENCFF001IHX fastq reads ENCSR000AIM ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus SRF-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 301899546 Barbara Wold, Caltech 77b4e8e8d737636a695b0150692c9f1e https://www.encodeproject.org/files/ENCFF001IHX/@@download/ENCFF001IHX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001IHY fastq reads ENCSR000AIM ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus SRF-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 335648847 Barbara Wold, Caltech af741bed9a9f26f0c5b6cafb8a62f974 https://www.encodeproject.org/files/ENCFF001IHY/@@download/ENCFF001IHY.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001IHZ fastq reads ENCSR000AIM ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus SRF-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 302622439 Barbara Wold, Caltech dca9e35fea8df011c88b9dc7dfd5f085 https://www.encodeproject.org/files/ENCFF001IHZ/@@download/ENCFF001IHZ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001MTM fastq reads 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 2 1 36 single-ended 402857263 Ross Hardison, PennState e0f1b28b34d6313a59b7f7f06328ce29 https://www.encodeproject.org/files/ENCFF001MTM/@@download/ENCFF001MTM.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSW/ released low read length, inconsistent control read length, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001MTO fastq reads 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 1 36 single-ended 949249241 Ross Hardison, PennState b7292d33c5b4f3eca34ac2b678494bc8 https://www.encodeproject.org/files/ENCFF001MTO/@@download/ENCFF001MTO.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSM/ released low read length, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001MOI fastq reads ENCSR000DIE ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA2-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 36 single-ended 607479209 Ross Hardison, PennState 03208b484979faeebc8888ef15c6f8cb https://www.encodeproject.org/files/ENCFF001MOI/@@download/ENCFF001MOI.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MOR/ released low read length, low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001MOP fastq reads ENCSR000DIE ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA2-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 36 single-ended 598855193 Ross Hardison, PennState e83b2b76f35ed6c0574e5a7ae07a6a99 https://www.encodeproject.org/files/ENCFF001MOP/@@download/ENCFF001MOP.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MPG/ released low read length, low read depth, borderline replicate concordance, inconsistent control read length, inconsistent platforms biological replicates with identical biosample ENCFF001IIV fastq reads ENCSR000AIT ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1784114238 Barbara Wold, Caltech d2a3a76954e1b731276404dd7837b5cd https://www.encodeproject.org/files/ENCFF001IIV/@@download/ENCFF001IIV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001IFX fastq reads ENCSR000AIU ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 753641541 Barbara Wold, Caltech c42bc9afc1c8f9096f8fa020d5b49605 https://www.encodeproject.org/files/ENCFF001IFX/@@download/ENCFF001IFX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth insufficient read length ENCFF001IFY fastq reads ENCSR000AIU ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 816435375 Barbara Wold, Caltech f2e59b403158c5553e1fec532a795d11 https://www.encodeproject.org/files/ENCFF001IFY/@@download/ENCFF001IFY.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth insufficient read length ENCFF001IDX fastq reads ENCSR000AII ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus E2F4-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1096025730 Barbara Wold, Caltech b794c3409f9a6c2947a186ed6bc225f2 https://www.encodeproject.org/files/ENCFF001IDX/@@download/ENCFF001IDX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF001IIU fastq reads ENCSR000AIN ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus TCF12-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1318756530 Barbara Wold, Caltech 422fc27b552dd0be9a5620ff4fd5833b https://www.encodeproject.org/files/ENCFF001IIU/@@download/ENCFF001IIU.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released mild to moderate bottlenecking insufficient read depth, severe bottlenecking, poor library complexity ENCFF001IHC fastq reads ENCSR000AIR ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 307444369 Barbara Wold, Caltech d36a07f7c1c0cc506619be1f8c8ef3c7 https://www.encodeproject.org/files/ENCFF001IHC/@@download/ENCFF001IHC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001IHD fastq reads ENCSR000AIR ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 643114405 Barbara Wold, Caltech fcf02ecf04a183a5acbc646c9fc9deab https://www.encodeproject.org/files/ENCFF001IHD/@@download/ENCFF001IHD.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001IHE fastq reads ENCSR000AIR ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 623905069 Barbara Wold, Caltech 23073811836324ee3abed2b8bf1aaad4 https://www.encodeproject.org/files/ENCFF001IHE/@@download/ENCFF001IHE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IDS/, /files/ENCFF001IDT/, /files/ENCFF001IDU/, /files/ENCFF001IDV/ released low read depth insufficient read length ENCFF001IFS fastq reads ENCSR000AIX ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus POLR2A-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 701466814 Barbara Wold, Caltech 7f3c46009e4b62f6bfd78f6067254874 https://www.encodeproject.org/files/ENCFF001IFS/@@download/ENCFF001IFS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking, moderate library complexity insufficient read length ENCFF001IFT fastq reads ENCSR000AIX ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus POLR2A-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 656146691 Barbara Wold, Caltech 7adbaf4d55d962f1e3206850ae89dd7b https://www.encodeproject.org/files/ENCFF001IFT/@@download/ENCFF001IFT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking, moderate library complexity insufficient read length ENCFF001IGT fastq reads ENCSR000AIF ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 247106585 Barbara Wold, Caltech 3983b946d25c7fe3ea37bb53db932a30 https://www.encodeproject.org/files/ENCFF001IGT/@@download/ENCFF001IGT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released insufficient read length extremely low read depth ENCFF001IGU fastq reads ENCSR000AIF ChIP-seq EFO:0001098 C2C12 cell line Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 162862224 Barbara Wold, Caltech e4ca2324f50c9a520ab639336b9ee8d6 https://www.encodeproject.org/files/ENCFF001IGU/@@download/ENCFF001IGU.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released insufficient read length extremely low read depth ENCFF001NQU fastq reads 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 1 36 single-ended 971475366 Michael Snyder, Stanford 0aff2ad97e02a628bdc8c77e1295893e https://www.encodeproject.org/files/ENCFF001NQU/@@download/ENCFF001NQU.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTS/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NQW fastq reads 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 2 1 36 single-ended 943303315 Michael Snyder, Stanford a81c6f1a8beb3cc77c48e3f6f4744b76 https://www.encodeproject.org/files/ENCFF001NQW/@@download/ENCFF001NQW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTU/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001MSV fastq reads 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 1 36 single-ended 672292682 Ross Hardison, PennState 4ce38cf1ae9c5e5fb411592cd025479a https://www.encodeproject.org/files/ENCFF001MSV/@@download/ENCFF001MSV.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSM/ released low read length, low read depth, inconsistent platforms missing raw data in replicate, biological replicates with identical biosample ENCFF001MSX fastq reads 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 2 1 36 single-ended 558797102 Ross Hardison, PennState c71e503a65e500f1e10bcabf977170fd https://www.encodeproject.org/files/ENCFF001MSX/@@download/ENCFF001MSX.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSW/ archived low read length, low read depth, inconsistent control read length, inconsistent platforms missing raw data in replicate, biological replicates with identical biosample ENCFF001MTE fastq reads 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 3 1 36 single-ended 757932126 Ross Hardison, PennState 4351f9ccd2005630d560b7bb33d153ec https://www.encodeproject.org/files/ENCFF001MTE/@@download/ENCFF001MTE.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSW/ released low read length, low read depth, inconsistent control read length, inconsistent platforms missing raw data in replicate, biological replicates with identical biosample ENCFF001MNC fastq reads ENCSR000DIB ChIP-seq CL:0000765 erythroblast primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 41 single-ended 1419494061 Ross Hardison, PennState e9eb3ca9cd8b04af4776e4d11a5691c1 https://www.encodeproject.org/files/ENCFF001MNC/@@download/ENCFF001MNC.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MMU/ released low read length, mixed read lengths, inconsistent platforms ENCFF001MNJ fastq reads ENCSR000DIB ChIP-seq CL:0000765 erythroblast primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 3 1 55 single-ended 4875290074 Ross Hardison, PennState ee504f0add00cb01f9559122c27f9831 https://www.encodeproject.org/files/ENCFF001MNJ/@@download/ENCFF001MNJ.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MMW/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms ENCFF001MNL fastq reads ENCSR000DIB ChIP-seq CL:0000765 erythroblast primary cell Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 55 single-ended 5773488169 Ross Hardison, PennState 58444d05e92e8650890947ef9e882e88 https://www.encodeproject.org/files/ENCFF001MNL/@@download/ENCFF001MNL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MMW/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms ENCFF002ARM fastq reads ENCSR392DGA ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus POU5F1-mouse DNA see document see document False 2014-03-17 ENCODE 1 1 48 single-ended 2909663437 Ross Hardison, PennState a5c5d3acd32093dc8651ba21cb35b59c https://www.encodeproject.org/files/ENCFF002ARM/@@download/ENCFF002ARM.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGK/ released low read length, inconsistent control read length, borderline replicate concordance experiment not submitted to GEO ENCFF002ARO fastq reads ENCSR392DGA ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus POU5F1-mouse DNA see document see document False 2014-03-17 ENCODE 2 1 48 single-ended 2408184776 Ross Hardison, PennState e2135b882d2d8aa45742183ddfe1a5f4 https://www.encodeproject.org/files/ENCFF002ARO/@@download/ENCFF002ARO.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGM/ released low read length, inconsistent control read length, borderline replicate concordance experiment not submitted to GEO ENCFF001IGL fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 354505514 Barbara Wold, Caltech ab3de5ee627beead9f205872d0804df4 https://www.encodeproject.org/files/ENCFF001IGL/@@download/ENCFF001IGL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001IGM fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 468789419 Barbara Wold, Caltech d1f4b24c557959ebb259576a66c2c303 https://www.encodeproject.org/files/ENCFF001IGM/@@download/ENCFF001IGM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001IGN fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 569539236 Barbara Wold, Caltech 04479943668dadbb10e2c0a6edc12665 https://www.encodeproject.org/files/ENCFF001IGN/@@download/ENCFF001IGN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001IGO fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 409630624 Barbara Wold, Caltech bb2fe9f30ca70354a3df29cf49e72345 https://www.encodeproject.org/files/ENCFF001IGO/@@download/ENCFF001IGO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001IGP fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 350416581 Barbara Wold, Caltech 1b4ff10730de588c66174eba18481e24 https://www.encodeproject.org/files/ENCFF001IGP/@@download/ENCFF001IGP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001IGQ fastq reads ENCSR000AIC ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOG-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 361993040 Barbara Wold, Caltech c9c3d293a70231cc4c5dc26bb6b0e39f https://www.encodeproject.org/files/ENCFF001IGQ/@@download/ENCFF001IGQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released low read depth, mild to moderate bottlenecking insufficient read length ENCFF001ICX fastq reads 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 1 50 single-ended 1240921929 Barbara Wold, Caltech dfd51e8b8085f88f932fb39a06ef0104 https://www.encodeproject.org/files/ENCFF001ICX/@@download/ENCFF001ICX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF001IDC fastq reads ENCSR000AIB ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus CEBPB-mouse DNA see document see document False 2011-11-23 ENCODE 2 1 50 single-ended 1063634878 Barbara Wold, Caltech b892c626867f7786070f89cced35838e https://www.encodeproject.org/files/ENCFF001IDC/@@download/ENCFF001IDC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEZ/ released mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample insufficient read depth, severe bottlenecking, poor library complexity ENCFF001IIH fastq reads ENCSR000AIP ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus TCF3-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 495853863 Barbara Wold, Caltech 50141b166155402169a7730a09fa2c56 https://www.encodeproject.org/files/ENCFF001IIH/@@download/ENCFF001IIH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released insufficient read depth, insufficient read length ENCFF001III fastq reads ENCSR000AIP ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus TCF3-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 490321587 Barbara Wold, Caltech 29f88c2bcc6f9d3e92acc8281ce80c11 https://www.encodeproject.org/files/ENCFF001III/@@download/ENCFF001III.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released insufficient read depth, insufficient read length ENCFF001IIY fastq reads ENCSR000AIQ ChIP-seq EFO:0001098 C2C12 cell line Mus musculus USF1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1339549842 Barbara Wold, Caltech 681efd1b1d4497a0a69aaf84925de5fb https://www.encodeproject.org/files/ENCFF001IIY/@@download/ENCFF001IIY.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IFD/ released low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001IGF fastq reads ENCSR000AIL ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MAX-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 50 single-ended 1131571291 Barbara Wold, Caltech 692b6156dd527c2bb75f6a8ac82cc030 https://www.encodeproject.org/files/ENCFF001IGF/@@download/ENCFF001IGF.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEY/ released low read depth, mild to moderate bottlenecking ENCFF001IDG fastq reads ENCSR000AIJ ChIP-seq EFO:0001098 C2C12 cell line Mus musculus CTCF-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 306507691 Barbara Wold, Caltech 14e46768a62b3240f119f0a39b507f1e https://www.encodeproject.org/files/ENCFF001IDG/@@download/ENCFF001IDG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released insufficient read depth, insufficient read length ENCFF001IDH fastq reads ENCSR000AIJ ChIP-seq EFO:0001098 C2C12 cell line Mus musculus CTCF-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 537117380 Barbara Wold, Caltech 01e97f13c88fb2348614682669c809b8 https://www.encodeproject.org/files/ENCFF001IDH/@@download/ENCFF001IDH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEG/, /files/ENCFF001IEH/, /files/ENCFF001IEI/ released insufficient read depth, insufficient read length ENCFF001IHI fastq reads ENCSR000AIH ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 1049096703 Barbara Wold, Caltech 846dcb76a1d781ff969c46df0491c37c https://www.encodeproject.org/files/ENCFF001IHI/@@download/ENCFF001IHI.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released mild to moderate bottlenecking insufficient read length ENCFF001IHJ fastq reads ENCSR000AIH ChIP-seq CL:0000187 myocyte in vitro differentiated cells Mus musculus MYOD1-mouse DNA see document see document False 2011-11-23 ENCODE 1 1 32 single-ended 714543991 Barbara Wold, Caltech 23fed2b339daaaaca52c7f1657c63ba5 https://www.encodeproject.org/files/ENCFF001IHJ/@@download/ENCFF001IHJ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001IEA/, /files/ENCFF001IEB/, /files/ENCFF001IEC/, /files/ENCFF001IED/, /files/ENCFF001IEE/ released mild to moderate bottlenecking insufficient read length ENCFF001MQR fastq reads ENCSR000DHC ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 41 single-ended 1472002883 Ross Hardison, PennState f8f115092c5f367f9261389344989732 https://www.encodeproject.org/files/ENCFF001MQR/@@download/ENCFF001MQR.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MRP/ released low read length, inconsistent control read length, inconsistent platforms ENCFF001LJQ fastq reads ENCSR000CCC ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 822306699 Bing Ren, UCSD b00a97de03447952720798bede9cc04a https://www.encodeproject.org/files/ENCFF001LJQ/@@download/ENCFF001LJQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KEX/ released low read length, borderline replicate concordance insufficient read depth ENCFF001MOZ fastq reads ENCSR000DIG ChIP-seq EFO:0002034 G1E stem cell Mus musculus POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 36 single-ended 656384502 Ross Hardison, PennState bfb161fce38c72de2613b2fbb270215a https://www.encodeproject.org/files/ENCFF001MOZ/@@download/ENCFF001MOZ.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MOR/ released low read length, low read depth, inconsistent platforms biological replicates with identical biosample insufficient replicate concordance ENCFF001MPE fastq reads ENCSR000DIG ChIP-seq EFO:0002034 G1E stem cell Mus musculus POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 36 single-ended 756936913 Ross Hardison, PennState b775d7cede438636de04c28dd1105d5b https://www.encodeproject.org/files/ENCFF001MPE/@@download/ENCFF001MPE.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MPG/ released low read length, low read depth, inconsistent control read length, inconsistent platforms biological replicates with identical biosample insufficient replicate concordance ENCFF001MUJ fastq reads ENCSR000DIJ ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 41 single-ended 1332709847 Ross Hardison, PennState 8f3fba6741cb9ec4940bc041c6a66a89 https://www.encodeproject.org/files/ENCFF001MUJ/@@download/ENCFF001MUJ.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MUT/ released low read length, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MUM fastq reads ENCSR000DIJ ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 3 1 45 single-ended 2132036352 Ross Hardison, PennState 3a75f406f665c722d94b844fe066015d https://www.encodeproject.org/files/ENCFF001MUM/@@download/ENCFF001MUM.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample ENCFF001MUP fastq reads ENCSR000DIJ ChIP-seq CL:0000556 megakaryocyte primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 55 single-ended 4519972158 Ross Hardison, PennState 633085f27acbb716c4629dd093383aac https://www.encodeproject.org/files/ENCFF001MUP/@@download/ENCFF001MUP.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MUW/ released low read length, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MSD fastq reads 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 1 36 single-ended 448992400 Ross Hardison, PennState 5e66b53545c7066dda46d73a62b52f24 https://www.encodeproject.org/files/ENCFF001MSD/@@download/ENCFF001MSD.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSM/ released low read length, inconsistent platforms biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF001MSI fastq reads 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 2 1 36 single-ended 595263632 Ross Hardison, PennState bbc6f0394807ff7cd0f014e61f943a9f https://www.encodeproject.org/files/ENCFF001MSI/@@download/ENCFF001MSI.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSW/ released low read length, inconsistent control read length, inconsistent platforms biological replicates with identical biosample insufficient read depth, insufficient replicate concordance ENCFF001NNF fastq reads ENCSR000ERJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF2-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1106901097 Michael Snyder, Stanford 3edf8b246c97a17eb6cf2a9a13d36979 https://www.encodeproject.org/files/ENCFF001NNF/@@download/ENCFF001NNF.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth ENCFF001NNM fastq reads ENCSR000ERJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF2-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1614085096 Michael Snyder, Stanford a62d9a6914579ee39df4aea426a2f3d7 https://www.encodeproject.org/files/ENCFF001NNM/@@download/ENCFF001NNM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth ENCFF001MNP fastq reads ENCSR000DIS ChIP-seq EFO:0002034 G1E stem cell Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 36 single-ended 564774383 Ross Hardison, PennState 9075ac7bcb26c6ad9c92e5729e27523e https://www.encodeproject.org/files/ENCFF001MNP/@@download/ENCFF001MNP.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MOR/ released low read length, low read depth, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MNV fastq reads ENCSR000DIS ChIP-seq EFO:0002034 G1E stem cell Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 41 single-ended 1107370733 Ross Hardison, PennState cab53378da43a11ab9a3c918927e9a4c https://www.encodeproject.org/files/ENCFF001MNV/@@download/ENCFF001MNV.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MPG/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample ENCFF001NSC fastq reads 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 1 36 single-ended 769527070 Michael Snyder, Stanford d954e3cfeed2db29c854000c359582d7 https://www.encodeproject.org/files/ENCFF001NSC/@@download/ENCFF001NSC.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTS/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NSE fastq reads 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 2 1 36 single-ended 841891121 Michael Snyder, Stanford 8e9acde6edbcc61c54223c7226538454 https://www.encodeproject.org/files/ENCFF001NSE/@@download/ENCFF001NSE.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTU/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001LOC fastq reads ENCSR000CBT ChIP-seq UBERON:0002048 lung tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 285242199 Bing Ren, UCSD 870ffd53434093858490f1c0ca2d60d0 https://www.encodeproject.org/files/ENCFF001LOC/@@download/ENCFF001LOC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KOQ/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance extremely low read depth ENCFF001LOH fastq reads ENCSR000CBT ChIP-seq UBERON:0002048 lung tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 907765095 Bing Ren, UCSD 774ac4e9d99baacb0212eb60dee5b400 https://www.encodeproject.org/files/ENCFF001LOH/@@download/ENCFF001LOH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KOV/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance extremely low read depth ENCFF435VYL fastq reads ENCSR604XDL ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus MAFK-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 567589765 Michael Snyder, Stanford 459f6fe1b1819385f3e87febc337e42e https://www.encodeproject.org/files/ENCFF435VYL/@@download/ENCFF435VYL.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNN/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth ENCFF274DXL fastq reads ENCSR604XDL ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus MAFK-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 998637992 Michael Snyder, Stanford 634f9df0dd9a88c1de1725eab096b5fa https://www.encodeproject.org/files/ENCFF274DXL/@@download/ENCFF274DXL.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNP/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample insufficient read depth ENCFF548AXA fastq reads ENCSR527DME ChIP-seq UBERON:0002048 lung tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 2 1 50 single-ended 1380010561 Richard Myers, HAIB 145a296f07382bcd552003ab0d5d759e SRA:SRR5111731 https://www.encodeproject.org/files/ENCFF548AXA/@@download/ENCFF548AXA.fastq.gz Illumina HiSeq 2000 /files/ENCFF876HRO/ released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF482ODC fastq reads ENCSR527DME ChIP-seq UBERON:0002048 lung tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1 1 50 single-ended 1728830966 Richard Myers, HAIB d21138a6302425e019bd8c89e05b4424 SRA:SRR5111730 https://www.encodeproject.org/files/ENCFF482ODC/@@download/ENCFF482ODC.fastq.gz Illumina HiSeq 2000 /files/ENCFF876HRO/ released mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF001NLZ fastq reads ENCSR000EQQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 1019828534 Michael Snyder, Stanford c76e33c218bb9c3ce749b806d67f83b4 https://www.encodeproject.org/files/ENCFF001NLZ/@@download/ENCFF001NLZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF001NMB fastq reads ENCSR000EQQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1044399104 Michael Snyder, Stanford 35107279e8ebca380b3282154b625fe6 https://www.encodeproject.org/files/ENCFF001NMB/@@download/ENCFF001NMB.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF001NLB fastq reads ENCSR000ERK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RAD21-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1207886069 Michael Snyder, Stanford bed597cc700dd305c35c0144b51c94d4 https://www.encodeproject.org/files/ENCFF001NLB/@@download/ENCFF001NLB.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001NLC fastq reads ENCSR000ERK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RAD21-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1107395945 Michael Snyder, Stanford 5572b34bbdc3d716fce385b058841637 https://www.encodeproject.org/files/ENCFF001NLC/@@download/ENCFF001NLC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF096EGJ fastq reads ENCSR397RHW ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1025246041 Richard Myers, HAIB 66467ed21327954b452a92a13adf11d3 SRA:SRR5111533 https://www.encodeproject.org/files/ENCFF096EGJ/@@download/ENCFF096EGJ.fastq.gz Illumina HiSeq 2000 /files/ENCFF331QQL/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF803MRJ fastq reads ENCSR397RHW ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1083660814 Richard Myers, HAIB 83120264679b69e2e67591356b17ed60 SRA:SRR5111532 https://www.encodeproject.org/files/ENCFF803MRJ/@@download/ENCFF803MRJ.fastq.gz Illumina HiSeq 2000 /files/ENCFF331QQL/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NYF fastq reads 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 1 36 single-ended 866315037 Michael Snyder, Stanford 25f04432deee10aa54c04972f40529ce https://www.encodeproject.org/files/ENCFF001NYF/@@download/ENCFF001NYF.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001NYK fastq reads ENCSR000EUC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2A-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1057296684 Michael Snyder, Stanford 4b0a5dcfa3d26a01edc05f324216fd18 https://www.encodeproject.org/files/ENCFF001NYK/@@download/ENCFF001NYK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF423RCQ fastq reads ENCSR867SDZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 893122499 Michael Snyder, Stanford 607c533c9a166ddeecd058c2d19ab404 https://www.encodeproject.org/files/ENCFF423RCQ/@@download/ENCFF423RCQ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample severe bottlenecking, poor library complexity, insufficient replicate concordance extremely low read depth ENCFF433FQJ fastq reads ENCSR867SDZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MEF2A-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 633473223 Michael Snyder, Stanford 3e49a5a2075545570f3a0c0d3c3c3e3a https://www.encodeproject.org/files/ENCFF433FQJ/@@download/ENCFF433FQJ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample severe bottlenecking, poor library complexity, insufficient replicate concordance extremely low read depth ENCFF592ERV fastq reads ENCSR033OWC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 845099169 Michael Snyder, Stanford 85320f303673650d550ad436f868b88d https://www.encodeproject.org/files/ENCFF592ERV/@@download/ENCFF592ERV.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF186NAS fastq reads ENCSR033OWC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 746822664 Michael Snyder, Stanford 076cf403ab2c9574bcd6840a69e8629f https://www.encodeproject.org/files/ENCFF186NAS/@@download/ENCFF186NAS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF537ACV fastq reads ENCSR906QEK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 752589282 Michael Snyder, Stanford 94aeacafd015e30a03a20970875448d2 https://www.encodeproject.org/files/ENCFF537ACV/@@download/ENCFF537ACV.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF453MVP fastq reads ENCSR906QEK ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 489295777 Michael Snyder, Stanford 1e4e4879547294300ca75acbf35e6b64 https://www.encodeproject.org/files/ENCFF453MVP/@@download/ENCFF453MVP.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF001NKE fastq reads ENCSR000ERQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2A-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 650470421 Michael Snyder, Stanford 31b14a3202d378c267a2d5e2ba810053 https://www.encodeproject.org/files/ENCFF001NKE/@@download/ENCFF001NKE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NKF fastq reads ENCSR000ERQ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2A-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 903742161 Michael Snyder, Stanford 48d2e4d630f76556aedfd87e7444f358 https://www.encodeproject.org/files/ENCFF001NKF/@@download/ENCFF001NKF.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NGZ fastq reads ENCSR000EQU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus KAT2A-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 990815467 Michael Snyder, Stanford dd8c2ecf15a343ff6f891260e9be65c2 https://www.encodeproject.org/files/ENCFF001NGZ/@@download/ENCFF001NGZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms insufficient replicate concordance ENCFF001NHB fastq reads ENCSR000EQU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus KAT2A-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1158186924 Michael Snyder, Stanford c87b908d060998922e6eba92feeaf437 https://www.encodeproject.org/files/ENCFF001NHB/@@download/ENCFF001NHB.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms insufficient replicate concordance ENCFF529HKW fastq reads ENCSR531HWD ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus CHD2-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 814257699 Michael Snyder, Stanford 7c9995a3788521b417a445a7ae4b07a4 https://www.encodeproject.org/files/ENCFF529HKW/@@download/ENCFF529HKW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNP/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF254ZVV fastq reads ENCSR531HWD ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus CHD2-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 1199139199 Michael Snyder, Stanford 957dbdca3716f4959c5a102ae5e31a00 https://www.encodeproject.org/files/ENCFF254ZVV/@@download/ENCFF254ZVV.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNN/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF001NIA fastq reads ENCSR000ERB ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAFK-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1310165379 Michael Snyder, Stanford f62994515a5d09a7d293452cadbc72da https://www.encodeproject.org/files/ENCFF001NIA/@@download/ENCFF001NIA.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, borderline replicate concordance ENCFF001NIC fastq reads ENCSR000ERB ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAFK-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1254153649 Michael Snyder, Stanford 96dfb01dab77c3fc0f454e57f2414bef https://www.encodeproject.org/files/ENCFF001NIC/@@download/ENCFF001NIC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, borderline replicate concordance ENCFF001MWX fastq reads 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 1 41 single-ended 1477514484 Ross Hardison, PennState 957ac3da3ba301bc7e1ee194b32cf332 https://www.encodeproject.org/files/ENCFF001MWX/@@download/ENCFF001MWX.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MWB/ released mild to moderate bottlenecking, mixed read lengths, inconsistent control read length, low read length, moderate library complexity, inconsistent platforms ENCFF001MXC fastq reads ENCSR000DIA ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TAL1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 55 single-ended 2725715801 Ross Hardison, PennState 3b37889a8625303f5c7eb651ed7b50b3 https://www.encodeproject.org/files/ENCFF001MXC/@@download/ENCFF001MXC.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MWM/ released low read length, moderate library complexity, mild to moderate bottlenecking, mixed read lengths, inconsistent platforms ENCFF001NIG fastq reads ENCSR000ERR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUND-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1054017987 Michael Snyder, Stanford 8fbeeae6fc3e91ccbbc7322aa6ee31a2 https://www.encodeproject.org/files/ENCFF001NIG/@@download/ENCFF001NIG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001NIL fastq reads ENCSR000ERR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUND-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1103743125 Michael Snyder, Stanford 5665ae28fa07e4b7ccc93f6674054188 https://www.encodeproject.org/files/ENCFF001NIL/@@download/ENCFF001NIL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001LLV fastq reads ENCSR000CEB ChIP-seq UBERON:0002101 limb tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 30 single-ended 379068820 Bing Ren, UCSD 8b30aab1e0b73212012690f6b39899a8 https://www.encodeproject.org/files/ENCFF001LLV/@@download/ENCFF001LLV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KLI/ archived mild to moderate bottlenecking, inconsistent platforms insufficient read depth, severe bottlenecking, poor library complexity, insufficient read length extremely low read depth ENCFF001LLY fastq reads ENCSR000CEB ChIP-seq UBERON:0002101 limb tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 30 single-ended 914808631 Bing Ren, UCSD f9d59cca1ae133f7f6289c5a4951ece5 https://www.encodeproject.org/files/ENCFF001LLY/@@download/ENCFF001LLY.fastq.gz Illumina HiSeq 2000 /files/ENCFF044CWG/ archived mild to moderate bottlenecking, inconsistent control read length, inconsistent platforms insufficient read depth, severe bottlenecking, poor library complexity, insufficient read length extremely low read depth ENCFF001NGC fastq reads ENCSR000ERN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MYC-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1096763904 Michael Snyder, Stanford 251314891177bc2b02cc871f1679e356 https://www.encodeproject.org/files/ENCFF001NGC/@@download/ENCFF001NGC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NGO fastq reads ENCSR000ERN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MYC-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 995567119 Michael Snyder, Stanford e8ffa801aab6d94b79165263aea8087d https://www.encodeproject.org/files/ENCFF001NGO/@@download/ENCFF001NGO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001MMD fastq reads ENCSR000DIH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus PAX5-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 41 single-ended 1447608138 Ross Hardison, PennState 9a16d0d5e4cfc78189f04a81e48afcd0 https://www.encodeproject.org/files/ENCFF001MMD/@@download/ENCFF001MMD.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MLS/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms ENCFF001MMH fastq reads ENCSR000DIH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus PAX5-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 55 single-ended 3056317484 Ross Hardison, PennState 5c858d8a6d5ea1e35d4ad3872a435e8a https://www.encodeproject.org/files/ENCFF001MMH/@@download/ENCFF001MMH.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MLY/ released low read length, mixed read lengths, inconsistent platforms ENCFF001LQY fastq reads ENCSR000CBY ChIP-seq UBERON:0002106 spleen tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 30 single-ended 526337920 Bing Ren, UCSD 8948a3cedaaaf925cd4fcf3543189c7f https://www.encodeproject.org/files/ENCFF001LQY/@@download/ENCFF001LQY.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KVR/ released mild to moderate bottlenecking, inconsistent control read length, inconsistent platforms insufficient read depth, insufficient read length extremely low read depth ENCFF001LRE fastq reads ENCSR000CBY ChIP-seq UBERON:0002106 spleen tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 30 single-ended 612267265 Bing Ren, UCSD 3c7ecddc91aeddb64776ac104667427d https://www.encodeproject.org/files/ENCFF001LRE/@@download/ENCFF001LRE.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KWE/ released mild to moderate bottlenecking, inconsistent platforms insufficient read depth, insufficient read length extremely low read depth ENCFF001LQH fastq reads ENCSR000CED ChIP-seq UBERON:0002108 small intestine tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 30 single-ended 356110106 Bing Ren, UCSD fd5bcc1d64b81df01996b75a81a33d1f https://www.encodeproject.org/files/ENCFF001LQH/@@download/ENCFF001LQH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KUJ/ released mild to moderate bottlenecking, mixed read lengths, inconsistent control read length, low read length, low read depth, moderate library complexity, inconsistent platforms insufficient replicate concordance, insufficient read length extremely low read depth ENCFF001LQI fastq reads ENCSR000CED ChIP-seq UBERON:0002108 small intestine tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1482667027 Bing Ren, UCSD b912f261dd2a6b92f38de945fc532672 https://www.encodeproject.org/files/ENCFF001LQI/@@download/ENCFF001LQI.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KUK/ released mild to moderate bottlenecking, mixed read lengths, low read length, low read depth, moderate library complexity, inconsistent platforms insufficient replicate concordance, insufficient read length extremely low read depth ENCFF001NQE fastq reads 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 1 36 single-ended 818690886 Michael Snyder, Stanford 1171f81073d78f04289d02421ca9b2e9 https://www.encodeproject.org/files/ENCFF001NQE/@@download/ENCFF001NQE.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NQH fastq reads ENCSR000ESI ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus RCOR1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1148847464 Michael Snyder, Stanford 74ec5d86b93eff416d65094628ad5e37 https://www.encodeproject.org/files/ENCFF001NQH/@@download/ENCFF001NQH.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001LSJ fastq reads ENCSR000CDZ ChIP-seq UBERON:0002370 thymus tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 256034181 Bing Ren, UCSD 6db797262ef5c927e52b6891089c98d1 https://www.encodeproject.org/files/ENCFF001LSJ/@@download/ENCFF001LSJ.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KYT/ released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth, poor library complexity extremely low read depth ENCFF001LSL fastq reads ENCSR000CDZ ChIP-seq UBERON:0002370 thymus tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 526849908 Bing Ren, UCSD 4bacf9cb69bbb97d7cb747def245f211 https://www.encodeproject.org/files/ENCFF001LSL/@@download/ENCFF001LSL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KYS/ released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth, poor library complexity extremely low read depth ENCFF001LLM fastq reads ENCSR000CBK ChIP-seq UBERON:0002113 kidney tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 824516883 Bing Ren, UCSD 0537221a1785e08a4730c9510e602e8d https://www.encodeproject.org/files/ENCFF001LLM/@@download/ENCFF001LLM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KKF/ released low read length, low read depth ENCFF001LIJ fastq reads ENCSR000CBO ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 841162261 Bing Ren, UCSD 20bf752c7fc880fa848a1eeee86352ef https://www.encodeproject.org/files/ENCFF001LIJ/@@download/ENCFF001LIJ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KCX/ released low read length, mild to moderate bottlenecking insufficient read depth extremely low read depth ENCFF001LIK fastq reads ENCSR000CBO ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 812102450 Bing Ren, UCSD 8d761617311470deca8077439eb3fe15 https://www.encodeproject.org/files/ENCFF001LIK/@@download/ENCFF001LIK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KDF/ released low read length, mild to moderate bottlenecking insufficient read depth extremely low read depth ENCFF001LJV fastq reads ENCSR000CBI ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 727262572 Bing Ren, UCSD c19df76966fc16da96cc7a1817f9bc3d https://www.encodeproject.org/files/ENCFF001LJV/@@download/ENCFF001LJV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIL/ released low read length, mild to moderate bottlenecking, mixed read lengths insufficient read depth, insufficient read length ENCFF001LJW fastq reads ENCSR000CBI ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 33 single-ended 559726846 Bing Ren, UCSD 150a94c66571075c8d7c93234c99265c https://www.encodeproject.org/files/ENCFF001LJW/@@download/ENCFF001LJW.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIM/ released low read length, mild to moderate bottlenecking, mixed read lengths, inconsistent control read length insufficient read depth, insufficient read length ENCFF001MRX fastq reads 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 1 36 single-ended 1261099639 Ross Hardison, PennState 7f77ac95f075cf8991f861c05e61c350 https://www.encodeproject.org/files/ENCFF001MRX/@@download/ENCFF001MRX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001MSM/ released low read length, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MSL fastq reads 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 2 1 55 single-ended 5759769099 Ross Hardison, PennState f5397ecb7935af5ff6b84f39fe2705bd https://www.encodeproject.org/files/ENCFF001MSL/@@download/ENCFF001MSL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MSW/ released low read length, mixed read lengths, inconsistent platforms biological replicates with identical biosample ENCFF001MQO fastq reads ENCSR000DGX ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 7 hour GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 41 single-ended 1376463661 Ross Hardison, PennState 27eed82facb2a01ee8f4fe16e9b5f7f6 https://www.encodeproject.org/files/ENCFF001MQO/@@download/ENCFF001MQO.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MRI/ released low read length, inconsistent control read length, inconsistent platforms ENCFF001LJN fastq reads ENCSR000CCD ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 697044760 Bing Ren, UCSD 842e5e09a0c545dc42cbe70ef42a8297 https://www.encodeproject.org/files/ENCFF001LJN/@@download/ENCFF001LJN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KEU/ released low read length insufficient read depth ENCFF001LJO fastq reads ENCSR000CCD ChIP-seq EFO:0005483 ES-Bruce4 stem cell Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 814014837 Bing Ren, UCSD 594481beb83ed1b95582f72a3c455764 https://www.encodeproject.org/files/ENCFF001LJO/@@download/ENCFF001LJO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KEX/ released low read length insufficient read depth ENCFF001NXQ fastq reads 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 1 36 single-ended 1054933775 Michael Snyder, Stanford 73614a27bce86fb5037ad04ff532b9d0 https://www.encodeproject.org/files/ENCFF001NXQ/@@download/ENCFF001NXQ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTD/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001NXS fastq reads 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 2 1 36 single-ended 950708384 Michael Snyder, Stanford 3d730aeb9419ed931cf5b658eeb39843 https://www.encodeproject.org/files/ENCFF001NXS/@@download/ENCFF001NXS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTF/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001NTK fastq reads ENCSR000EUG ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus GATA1-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 921190802 Michael Snyder, Stanford fa46374a09c29e7e95dd44f828e6682c https://www.encodeproject.org/files/ENCFF001NTK/@@download/ENCFF001NTK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NVE/ released low read length, low read depth biological replicates with identical biosample ENCFF001NTN fastq reads 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 1 36 single-ended 954638773 Michael Snyder, Stanford e62eccf5d396daf6a3d3cbbec8e55432 https://www.encodeproject.org/files/ENCFF001NTN/@@download/ENCFF001NTN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NVE/ released low read length, low read depth biological replicates with identical biosample ENCFF001MQL fastq reads ENCSR000DGZ ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 30 hour GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 55 single-ended 3106530238 Ross Hardison, PennState a250a47f04846259c8aaf75d3678cf3f https://www.encodeproject.org/files/ENCFF001MQL/@@download/ENCFF001MQL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MRC/ released inconsistent control read length ENCFF001NVW fastq reads 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 1 36 single-ended 767689481 Michael Snyder, Stanford 1850b9b47da77d5a2576b86de2b11d12 https://www.encodeproject.org/files/ENCFF001NVW/@@download/ENCFF001NVW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001NVZ fastq reads ENCSR000ESL ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAZ-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 799975072 Michael Snyder, Stanford 3c9048a96bbfd96dc326f01130147e4a https://www.encodeproject.org/files/ENCFF001NVZ/@@download/ENCFF001NVZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001MQJ fastq reads ENCSR000DGY ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 3 hour GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 41 single-ended 1491664196 Ross Hardison, PennState e0df3054745b02a795bbacb9458f4449 https://www.encodeproject.org/files/ENCFF001MQJ/@@download/ENCFF001MQJ.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MRH/ released low read length, inconsistent control read length, inconsistent platforms ENCFF001NKQ fastq reads ENCSR000EQY ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SIN3A-mouse DNA see document see document False 2012-06-15 ENCODE 1 1 36 single-ended 1280247499 Michael Snyder, Stanford b9e36b7ff3b896c553c37856a679242b https://www.encodeproject.org/files/ENCFF001NKQ/@@download/ENCFF001NKQ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, inconsistent platforms ENCFF001NKS fastq reads ENCSR000EQY ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SIN3A-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 1245250757 Michael Snyder, Stanford ddca465e7c9f6e1fb66420b07454df18 https://www.encodeproject.org/files/ENCFF001NKS/@@download/ENCFF001NKS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, inconsistent platforms ENCFF001NVQ fastq reads 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 1 36 single-ended 1096915730 Michael Snyder, Stanford 551d771460f19252ff0f57004d802032 https://www.encodeproject.org/files/ENCFF001NVQ/@@download/ENCFF001NVQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NVR fastq reads ENCSR000ETZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus JUND-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 955289943 Michael Snyder, Stanford b86c808a23e2c7cb214b4b4cc72792ed https://www.encodeproject.org/files/ENCFF001NVR/@@download/ENCFF001NVR.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001MMN fastq reads ENCSR000DIL ChIP-seq CL:0000765 erythroblast primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 41 single-ended 1454017901 Ross Hardison, PennState aea61365ec4d36dfc069a18a8c6835f1 https://www.encodeproject.org/files/ENCFF001MMN/@@download/ENCFF001MMN.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MMU/ released low read length, mixed read lengths, inconsistent platforms ENCFF001MMR fastq reads ENCSR000DIL ChIP-seq CL:0000765 erythroblast primary cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 55 single-ended 4259122986 Ross Hardison, PennState aa0c4fea1e9363807eb250de135bf26d https://www.encodeproject.org/files/ENCFF001MMR/@@download/ENCFF001MMR.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MMW/ released low read length, mixed read lengths, inconsistent control read length, inconsistent platforms ENCFF001ZQP fastq reads ENCSR362VNF ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus CTCF-mouse DNA see document see document False 2014-02-24 ENCODE 1 1 45 single-ended 2020172004 Ross Hardison, PennState e2c38e995d900af5e47f7a34e1697a53 https://www.encodeproject.org/files/ENCFF001ZQP/@@download/ENCFF001ZQP.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGK/ released low read length experiment not submitted to GEO ENCFF001ZQR fastq reads ENCSR362VNF ChIP-seq EFO:0007751 E14TG2a.4 stem cell Mus musculus CTCF-mouse DNA see document see document False 2014-02-24 ENCODE 2 1 45 single-ended 1881057794 Ross Hardison, PennState f671bc9e7c2d8675575d5fd5c34ef411 https://www.encodeproject.org/files/ENCFF001ZQR/@@download/ENCFF001ZQR.fastq.gz Illumina HiSeq 2000 /files/ENCFF001ZGM/ released low read length experiment not submitted to GEO ENCFF001NIP fastq reads ENCSR000EQT ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAZ-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 950892073 Michael Snyder, Stanford 201ab3402ae4068701aee662eaa580ec https://www.encodeproject.org/files/ENCFF001NIP/@@download/ENCFF001NIP.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001NIS fastq reads ENCSR000EQT ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAZ-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 887267779 Michael Snyder, Stanford 47855420b6223eb8847c4a781f06bdfd https://www.encodeproject.org/files/ENCFF001NIS/@@download/ENCFF001NIS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001NSQ fastq reads 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 1 36 single-ended 920487504 Michael Snyder, Stanford 6fb1baea7318694adb55067f654a9b39 https://www.encodeproject.org/files/ENCFF001NSQ/@@download/ENCFF001NSQ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001NSS fastq reads ENCSR000ESM ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus KAT2A-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1390380610 Michael Snyder, Stanford a4bd075033aef9015285de8d173d03d1 https://www.encodeproject.org/files/ENCFF001NSS/@@download/ENCFF001NSS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF332NMV fastq reads ENCSR418SBY ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1328071421 Richard Myers, HAIB 581c4b94f6a1150c4b82e1e3af1e29fc SRA:SRR5111581 https://www.encodeproject.org/files/ENCFF332NMV/@@download/ENCFF332NMV.fastq.gz Illumina HiSeq 2000 /files/ENCFF756GQQ/ released antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF657QHM fastq reads ENCSR418SBY ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1452650760 Richard Myers, HAIB d0b9ded6798473e446004863364350f9 SRA:SRR5111580 https://www.encodeproject.org/files/ENCFF657QHM/@@download/ENCFF657QHM.fastq.gz Illumina HiSeq 2000 /files/ENCFF756GQQ/ released antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001OBV fastq reads 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 1 36 single-ended 974772192 Michael Snyder, Stanford fb9d26d10984011d243061f2aa1c7977 https://www.encodeproject.org/files/ENCFF001OBV/@@download/ENCFF001OBV.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OBX fastq reads ENCSR000ESE ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZMIZ1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 866365282 Michael Snyder, Stanford 36f864e0da62ca9a96fa0a02848931fe https://www.encodeproject.org/files/ENCFF001OBX/@@download/ENCFF001OBX.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NJM fastq reads ENCSR000EQS ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus GABPA-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 1130929730 Michael Snyder, Stanford c7d2b85ab4668b64adb68ff65bdfe104 https://www.encodeproject.org/files/ENCFF001NJM/@@download/ENCFF001NJM.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms insufficient replicate concordance ENCFF001NJO fastq reads ENCSR000EQS ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus GABPA-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 935811781 Michael Snyder, Stanford 21ecfac1fa32f33b4fe504eb48841969 https://www.encodeproject.org/files/ENCFF001NJO/@@download/ENCFF001NJO.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms insufficient replicate concordance ENCFF001OBC fastq reads 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 1 36 single-ended 480656167 Michael Snyder, Stanford 9f16d28a89e0146d0fe8c5fe4072e236 https://www.encodeproject.org/files/ENCFF001OBC/@@download/ENCFF001OBC.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth biological replicates with identical biosample insufficient read depth ENCFF001OBJ fastq reads ENCSR000ETW ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF2-mouse DNA see document see document False 2011-02-07 ENCODE 2 1 36 single-ended 1233533866 Michael Snyder, Stanford e5e71ccd663350b9f202c8743bb0c0d9 https://www.encodeproject.org/files/ENCFF001OBJ/@@download/ENCFF001OBJ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth biological replicates with identical biosample insufficient read depth ENCFF001NZL fastq reads 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 1 36 single-ended 999039005 Michael Snyder, Stanford 4f3ce4fc460b29955f5b37f70dd80994 https://www.encodeproject.org/files/ENCFF001NZL/@@download/ENCFF001NZL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NZN fastq reads ENCSR000ETL ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus SMC3-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 839937253 Michael Snyder, Stanford 647f1b755b68e8cddcf5ef60b7d9fffa https://www.encodeproject.org/files/ENCFF001NZN/@@download/ENCFF001NZN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001OAK fastq reads 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 1 36 single-ended 1040353345 Michael Snyder, Stanford 3b0b2057afc1e08fc7d17d125da5309c https://www.encodeproject.org/files/ENCFF001OAK/@@download/ENCFF001OAK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth biological replicates with identical biosample ENCFF001OAL fastq reads ENCSR000EUB ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TBP-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 996866848 Michael Snyder, Stanford 5d029df4421309bd7f1a7d7fcf4f0205 https://www.encodeproject.org/files/ENCFF001OAL/@@download/ENCFF001OAL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NUK/ released low read length, low read depth biological replicates with identical biosample ENCFF001NSK fastq reads ENCSR000ETY ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus E2F4-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 891997675 Michael Snyder, Stanford 2fc8094f9680de41167f9f944bcbe339 https://www.encodeproject.org/files/ENCFF001NSK/@@download/ENCFF001NSK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF001NSL fastq reads 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 1 36 single-ended 1031236911 Michael Snyder, Stanford 6c76ac286ce5eea82d5888148e48e571 https://www.encodeproject.org/files/ENCFF001NSL/@@download/ENCFF001NSL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, borderline replicate concordance biological replicates with identical biosample ENCFF001NKM fastq reads ENCSR000ERH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 770143593 Michael Snyder, Stanford f93cdc73a6cb36d4a93e6f791c4411de https://www.encodeproject.org/files/ENCFF001NKM/@@download/ENCFF001NKM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001NKV fastq reads ENCSR000ERH ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 864060184 Michael Snyder, Stanford bb24d0316bfc106a93e2f4e66b2e4483 https://www.encodeproject.org/files/ENCFF001NKV/@@download/ENCFF001NKV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001NLH fastq reads ENCSR000ERG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SMC3-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 732841473 Michael Snyder, Stanford 35ff98b85dda13cad70e9afb22c6b988 https://www.encodeproject.org/files/ENCFF001NLH/@@download/ENCFF001NLH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001NLT fastq reads ENCSR000ERG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus SMC3-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 940503223 Michael Snyder, Stanford e9d358767db7ee3edf11e03c8aedc839 https://www.encodeproject.org/files/ENCFF001NLT/@@download/ENCFF001NLT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF381HVY fastq reads ENCSR980YXJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 792491525 Michael Snyder, Stanford 531595711b5ba4b28bbabcadff505430 https://www.encodeproject.org/files/ENCFF381HVY/@@download/ENCFF381HVY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF986XRF fastq reads ENCSR980YXJ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NRF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 861478492 Michael Snyder, Stanford 4bceb508e3ba4375c50b99937d4f3c04 https://www.encodeproject.org/files/ENCFF986XRF/@@download/ENCFF986XRF.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF001NPS fastq reads 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 1 36 single-ended 1034673954 Michael Snyder, Stanford 065bb6d26105b9936ac026c8d18eeb3a https://www.encodeproject.org/files/ENCFF001NPS/@@download/ENCFF001NPS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length biological replicates with identical biosample ENCFF001NPW fastq reads ENCSR000ETO ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CHD2-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1357566493 Michael Snyder, Stanford c0bc929e063529f94521abe9dd9ef229 https://www.encodeproject.org/files/ENCFF001NPW/@@download/ENCFF001NPW.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length biological replicates with identical biosample ENCFF001LMJ fastq reads ENCSR000CEC ChIP-seq UBERON:0002101 limb tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 30 single-ended 275637452 Bing Ren, UCSD 65cf38c7ece1bb54efb2f51bb5a6dce8 https://www.encodeproject.org/files/ENCFF001LMJ/@@download/ENCFF001LMJ.fastq.gz Illumina Genome Analyzer II /files/ENCFF044CWG/ released moderate library complexity, mild to moderate bottlenecking, inconsistent control read length, inconsistent platforms mismatched status insufficient read depth, insufficient read length extremely low read depth ENCFF001LMR fastq reads ENCSR000CEC ChIP-seq UBERON:0002101 limb tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 30 single-ended 604397421 Bing Ren, UCSD 3363bb3a2dec3ece411047fa6e36a88e https://www.encodeproject.org/files/ENCFF001LMR/@@download/ENCFF001LMR.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KLI/ released moderate library complexity, mild to moderate bottlenecking, inconsistent platforms mismatched status insufficient read depth, insufficient read length extremely low read depth ENCFF001NMP fastq reads ENCSR000EQO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 924136213 Michael Snyder, Stanford 66ae7802c84fc6688c87174a2d97dab7 https://www.encodeproject.org/files/ENCFF001NMP/@@download/ENCFF001NMP.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms ENCFF001NMS fastq reads ENCSR000EQO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1011661612 Michael Snyder, Stanford e48a04e9f8f5422ae79b2f5c1946d05f https://www.encodeproject.org/files/ENCFF001NMS/@@download/ENCFF001NMS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms ENCFF001MPZ fastq reads ENCSR000DHA ChIP-seq EFO:0002055 G1E-ER4 stem cell Mus musculus 17β-estradiol 10 nM 24 hour GATA1-mouse DNA see document see document False 2012-08-07 ENCODE 1 1 41 single-ended 1425444657 Ross Hardison, PennState 31554e22b8eb442f62e1d0cce8873d48 https://www.encodeproject.org/files/ENCFF001MPZ/@@download/ENCFF001MPZ.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MQZ/ released low read length, inconsistent control read length, inconsistent platforms ENCFF001NFO fastq reads ENCSR000ERF ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD2-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1038080396 Michael Snyder, Stanford ab7f5b455febbefc40bf1063881ffbdf https://www.encodeproject.org/files/ENCFF001NFO/@@download/ENCFF001NFO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF001NFP fastq reads ENCSR000ERF ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD2-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1065392168 Michael Snyder, Stanford e57e20c4b0626c35fde488f4280bd0e2 https://www.encodeproject.org/files/ENCFF001NFP/@@download/ENCFF001NFP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF001NWG fastq reads ENCSR000ETX ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAX-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1118627986 Michael Snyder, Stanford 444c45a755c5cc255b1e862f81d9d306 https://www.encodeproject.org/files/ENCFF001NWG/@@download/ENCFF001NWG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length biological replicates with identical biosample ENCFF001NWK fastq reads 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 1 36 single-ended 1491028464 Michael Snyder, Stanford 3489959098e292859c2e2984e0cef30b https://www.encodeproject.org/files/ENCFF001NWK/@@download/ENCFF001NWK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length biological replicates with identical biosample ENCFF001NYS fastq reads 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 1 36 single-ended 830401679 Michael Snyder, Stanford beffb9ed76538b0974ec0b40613fd892 https://www.encodeproject.org/files/ENCFF001NYS/@@download/ENCFF001NYS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NYW fastq reads 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 2 1 36 single-ended 834040149 Michael Snyder, Stanford 070f886a7b00767cf0c772c410c987e2 https://www.encodeproject.org/files/ENCFF001NYW/@@download/ENCFF001NYW.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF390DAS fastq reads ENCSR143WOK ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1195087204 Richard Myers, HAIB c90f9489a9f90ea5b9199ca6bc628d81 SRA:SRR5111187 https://www.encodeproject.org/files/ENCFF390DAS/@@download/ENCFF390DAS.fastq.gz Illumina HiSeq 2000 /files/ENCFF853NEA/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF837KZY fastq reads ENCSR143WOK ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 975495120 Richard Myers, HAIB dbf65d0e00339744349c0c3a2412933e SRA:SRR5111188 https://www.encodeproject.org/files/ENCFF837KZY/@@download/ENCFF837KZY.fastq.gz Illumina HiSeq 2000 /files/ENCFF853NEA/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF001NKH fastq reads ENCSR000ERI ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus EP300-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1275305507 Michael Snyder, Stanford 7e58dbc94286274a3c4a61183bd78ae8 https://www.encodeproject.org/files/ENCFF001NKH/@@download/ENCFF001NKH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF001NKK fastq reads ENCSR000ERI ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus EP300-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1656020766 Michael Snyder, Stanford 21303612cab8d0ba76199b7f28ac5ebb https://www.encodeproject.org/files/ENCFF001NKK/@@download/ENCFF001NKK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF001NSY fastq reads 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 1 36 single-ended 951578211 Michael Snyder, Stanford 5129e371c769e215603a22dc5163c872 https://www.encodeproject.org/files/ENCFF001NSY/@@download/ENCFF001NSY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NTA fastq reads ENCSR000ESG ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 821495820 Michael Snyder, Stanford a502c40f85516a4323ca84efb45c511e https://www.encodeproject.org/files/ENCFF001NTA/@@download/ENCFF001NTA.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NXB fastq reads 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 1 36 single-ended 856055810 Michael Snyder, Stanford 9551e07b32b081e6abb072e428d751ee https://www.encodeproject.org/files/ENCFF001NXB/@@download/ENCFF001NXB.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NXD fastq reads ENCSR000ETU ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus NELFE-mouse DNA see document see document False 2011-02-07 ENCODE 2 1 36 single-ended 932606529 Michael Snyder, Stanford e5a95b93924e21317079cfae7d5dc437 https://www.encodeproject.org/files/ENCFF001NXD/@@download/ENCFF001NXD.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001LPA fastq reads 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 1 36 single-ended 1857750780 Bing Ren, UCSD 9f7a9bc43db2b961e81c7af0afc1e11c https://www.encodeproject.org/files/ENCFF001LPA/@@download/ENCFF001LPA.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KRJ/ released low read length, mild to moderate bottlenecking insufficient read depth, severe bottlenecking, poor library complexity ENCFF001LPK fastq reads ENCSR000CFH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 3206007745 Bing Ren, UCSD 253f106c88a5b76658f4546a242089f7 https://www.encodeproject.org/files/ENCFF001LPK/@@download/ENCFF001LPK.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KRK/ released low read length, mild to moderate bottlenecking insufficient read depth, severe bottlenecking, poor library complexity ENCFF160DPX fastq reads ENCSR985ZTV ChIP-seq UBERON:0001891 midbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1098463981 Richard Myers, HAIB 465832429aad4619bda4baefaeead1b2 SRA:SRR5112343 https://www.encodeproject.org/files/ENCFF160DPX/@@download/ENCFF160DPX.fastq.gz Illumina HiSeq 2000 /files/ENCFF494VBT/ released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF323QPQ fastq reads ENCSR985ZTV ChIP-seq UBERON:0001891 midbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1638750335 Richard Myers, HAIB 5ef3412bf50e7d9040bd560abd09f431 SRA:SRR5112342 https://www.encodeproject.org/files/ENCFF323QPQ/@@download/ENCFF323QPQ.fastq.gz Illumina HiSeq 2000 /files/ENCFF494VBT/ released mild to moderate bottlenecking, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NMH fastq reads ENCSR000EQW ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZKSCAN1-mouse DNA see document see document False 2012-06-15 ENCODE 1 1 36 single-ended 942945902 Michael Snyder, Stanford f9ef097048d11fb47b7092b68f0fa3fa https://www.encodeproject.org/files/ENCFF001NMH/@@download/ENCFF001NMH.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, borderline replicate concordance, inconsistent platforms ENCFF001NMJ fastq reads ENCSR000EQW ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZKSCAN1-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 837366140 Michael Snyder, Stanford 6fd3c1a97f67a76cd7a242ff5a368375 https://www.encodeproject.org/files/ENCFF001NMJ/@@download/ENCFF001NMJ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, borderline replicate concordance, inconsistent platforms ENCFF001NNG fastq reads ENCSR000ERX ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 474459622 Michael Snyder, Stanford 3a2ae71c45eea2001640ab6ede5ae898 https://www.encodeproject.org/files/ENCFF001NNG/@@download/ENCFF001NNG.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNN/ released low read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001NNI fastq reads ENCSR000ERX ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1487005124 Michael Snyder, Stanford 434ffaaaf9c36d6c101d3ddb92b5a7ef https://www.encodeproject.org/files/ENCFF001NNI/@@download/ENCFF001NNI.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNP/ released low read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001NZS fastq reads ENCSR000ETS ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus RAD21-mouse DNA see document see document False 2011-02-07 ENCODE 2 1 36 single-ended 835436347 Michael Snyder, Stanford 3523e3c27d01397e59a374369a256e48 https://www.encodeproject.org/files/ENCFF001NZS/@@download/ENCFF001NZS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NZU fastq reads 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 1 36 single-ended 1048767076 Michael Snyder, Stanford dabb43efca28e1244177c31fcfa47aae https://www.encodeproject.org/files/ENCFF001NZU/@@download/ENCFF001NZU.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NFQ fastq reads ENCSR000ERO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUN-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 814965430 Michael Snyder, Stanford f18f1f3e36fbb19e57e63f6ec8cf3632 https://www.encodeproject.org/files/ENCFF001NFQ/@@download/ENCFF001NFQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF001NFT fastq reads ENCSR000ERO ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus JUN-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1024069586 Michael Snyder, Stanford 586b219a6344a877d53cf71f2c4f6f2f https://www.encodeproject.org/files/ENCFF001NFT/@@download/ENCFF001NFT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF001NZZ fastq reads 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 1 36 single-ended 981501386 Michael Snyder, Stanford b7bb2897c6e833cf8c346f97f4bc0cd0 https://www.encodeproject.org/files/ENCFF001NZZ/@@download/ENCFF001NZZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NUK/ released low read length, moderate library complexity, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001OAB fastq reads ENCSR000ESJ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus UBTF-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 885168689 Michael Snyder, Stanford 9c57726f8e8b5c0ea33cf3c98cfa106b https://www.encodeproject.org/files/ENCFF001OAB/@@download/ENCFF001OAB.fastq.gz Illumina Genome Analyzer /files/ENCFF001NUK/ released low read length, moderate library complexity, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF685COX fastq reads ENCSR104QEN ChIP-seq UBERON:0000945 stomach tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1017250765 Richard Myers, HAIB a885b6c7c5ecb73ece6493201a9c864e SRA:SRR5111151 https://www.encodeproject.org/files/ENCFF685COX/@@download/ENCFF685COX.fastq.gz Illumina HiSeq 2000 /files/ENCFF770PBO/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF671DZT fastq reads ENCSR104QEN ChIP-seq UBERON:0000945 stomach tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1277894350 Richard Myers, HAIB 644c5848a8ef826af1f6cc8ba3f9c922 SRA:SRR5111152 https://www.encodeproject.org/files/ENCFF671DZT/@@download/ENCFF671DZT.fastq.gz Illumina HiSeq 2000 /files/ENCFF770PBO/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF001NOS fastq reads 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 1 36 single-ended 907607812 Michael Snyder, Stanford da55e1e50bcf0187121c85ad587434f6 https://www.encodeproject.org/files/ENCFF001NOS/@@download/ENCFF001NOS.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms duplicate lane review, biological replicates with identical biosample ENCFF001NOU fastq reads ENCSR000ESH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus BHLHE40-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1296660609 Michael Snyder, Stanford 65ffe82aba3f17c49a4ec459bf16bb53 https://www.encodeproject.org/files/ENCFF001NOU/@@download/ENCFF001NOU.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms duplicate lane review, biological replicates with identical biosample ENCFF001MWI fastq reads 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 1 36 single-ended 604129003 Ross Hardison, PennState ce9652a5847c3b0e1e66ee7aa1299d8c https://www.encodeproject.org/files/ENCFF001MWI/@@download/ENCFF001MWI.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MWB/ released mild to moderate bottlenecking, mixed read lengths, low read length, low read depth, inconsistent platforms, borderline replicate concordance ENCFF001MWO fastq reads ENCSR000DHZ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2AphosphoS5-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 41 single-ended 1379900193 Ross Hardison, PennState 5153ac365af5150ebaaea40493684128 https://www.encodeproject.org/files/ENCFF001MWO/@@download/ENCFF001MWO.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MWM/ released mild to moderate bottlenecking, mixed read lengths, inconsistent control read length, low read length, low read depth, inconsistent platforms, borderline replicate concordance ENCFF051PSQ fastq reads ENCSR982LJQ ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1 1 50 single-ended 852699723 Richard Myers, HAIB 8d7419104a40d88e536e1e9fa30c9d84 SRA:SRR5112332 https://www.encodeproject.org/files/ENCFF051PSQ/@@download/ENCFF051PSQ.fastq.gz Illumina HiSeq 2000 /files/ENCFF286ECX/ released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF797QNA fastq reads ENCSR982LJQ ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 2 1 50 single-ended 936368635 Richard Myers, HAIB c1649907e4a03eaf4982f07ceadfd2b6 SRA:SRR5112333 https://www.encodeproject.org/files/ENCFF797QNA/@@download/ENCFF797QNA.fastq.gz Illumina HiSeq 2000 /files/ENCFF197BDN/ released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF524BAT fastq reads ENCSR677SIH ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1114272463 Richard Myers, HAIB 25c9181e232ffe373adf917e5d56be28 SRA:SRR5111943 https://www.encodeproject.org/files/ENCFF524BAT/@@download/ENCFF524BAT.fastq.gz Illumina HiSeq 2000 /files/ENCFF285EZB/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF472KEL fastq reads ENCSR677SIH ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 991464388 Richard Myers, HAIB 389c92becfef24c09cfa179c5482fcf7 SRA:SRR5111944 https://www.encodeproject.org/files/ENCFF472KEL/@@download/ENCFF472KEL.fastq.gz Illumina HiSeq 2000 /files/ENCFF285EZB/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NRO fastq reads ENCSR000ETQ ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CTCF-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 916820643 Michael Snyder, Stanford 58cae160a4926e589dbd9c89a132a8ac https://www.encodeproject.org/files/ENCFF001NRO/@@download/ENCFF001NRO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001NRQ fastq reads 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 1 36 single-ended 1162255225 Michael Snyder, Stanford 97248a1f5bcc75bc3c0e0d735cffc277 https://www.encodeproject.org/files/ENCFF001NRQ/@@download/ENCFF001NRQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF773SFT fastq reads ENCSR002ZAG ChIP-seq UBERON:0000160 intestine tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1321666970 Richard Myers, HAIB 7f1c4cccc441abb963b29c1f69601a0c SRA:SRR5111042 https://www.encodeproject.org/files/ENCFF773SFT/@@download/ENCFF773SFT.fastq.gz Illumina HiSeq 2000 /files/ENCFF691VJX/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF414VXY fastq reads ENCSR002ZAG ChIP-seq UBERON:0000160 intestine tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1275066259 Richard Myers, HAIB 6fea55c06b046aa8b7d2f4319738ef59 SRA:SRR5111041 https://www.encodeproject.org/files/ENCFF414VXY/@@download/ENCFF414VXY.fastq.gz Illumina HiSeq 2000 /files/ENCFF691VJX/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption, moderate library complexity NTR biosample, biological replicates with identical biosample ENCFF001LNS fastq reads ENCSR000CBV ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 880486987 Bing Ren, UCSD 44dd98606d96b8baf6c672f64df17c97 https://www.encodeproject.org/files/ENCFF001LNS/@@download/ENCFF001LNS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KOV/ released low read length, mild to moderate bottlenecking insufficient read depth ENCFF001LNT fastq reads ENCSR000CBV ChIP-seq UBERON:0002048 lung tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 870712159 Bing Ren, UCSD 358761a2b5d436ad8f2793879ae933e6 https://www.encodeproject.org/files/ENCFF001LNT/@@download/ENCFF001LNT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KOQ/ released low read length, mild to moderate bottlenecking insufficient read depth ENCFF001LHZ fastq reads ENCSR000CBQ ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 338545330 Bing Ren, UCSD c0ecd430586e0d9cced0ff16f723d705 https://www.encodeproject.org/files/ENCFF001LHZ/@@download/ENCFF001LHZ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KAK/ released low read length, borderline replicate concordance insufficient read depth ENCFF001LIB fastq reads ENCSR000CBQ ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 798656964 Bing Ren, UCSD c0bcd486e0fa66d7e27754f47495d2c1 https://www.encodeproject.org/files/ENCFF001LIB/@@download/ENCFF001LIB.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KAM/ released low read length, borderline replicate concordance insufficient read depth ENCFF001MOE fastq reads ENCSR000DIC ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 41 single-ended 1462106049 Ross Hardison, PennState 1b6eb374e03692c7d3dd31e4d472727f https://www.encodeproject.org/files/ENCFF001MOE/@@download/ENCFF001MOE.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MOR/ released low read length, mixed read lengths, inconsistent control read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001MOM fastq reads ENCSR000DIC ChIP-seq EFO:0002034 G1E stem cell Mus musculus GATA1-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 48 single-ended 5410047752 Ross Hardison, PennState da25b76b3d6485473a134f5959becbe2 https://www.encodeproject.org/files/ENCFF001MOM/@@download/ENCFF001MOM.fastq.gz Illumina HiSeq 2000 /files/ENCFF001MPG/ released low read length, mixed read lengths, inconsistent control read length, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001LQU fastq reads ENCSR000CEE ChIP-seq UBERON:0002108 small intestine tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 977574900 Bing Ren, UCSD 3d4ccd017c64d2c57bd17942ab017c48 https://www.encodeproject.org/files/ENCFF001LQU/@@download/ENCFF001LQU.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KUJ/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001LQW fastq reads ENCSR000CEE ChIP-seq UBERON:0002108 small intestine tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1852567088 Bing Ren, UCSD 17d6a24edc41c408b0076f9eac69b20e https://www.encodeproject.org/files/ENCFF001LQW/@@download/ENCFF001LQW.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KUK/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001LHN fastq reads ENCSR000CBN ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 996724043 Bing Ren, UCSD 487aad5c59ead18bcd561780a245dc11 https://www.encodeproject.org/files/ENCFF001LHN/@@download/ENCFF001LHN.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KAK/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth ENCFF001LHO fastq reads ENCSR000CBN ChIP-seq UBERON:0002037 cerebellum tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 908087695 Bing Ren, UCSD fc28d07269c86cceea6530810ac41489 https://www.encodeproject.org/files/ENCFF001LHO/@@download/ENCFF001LHO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KAM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth ENCFF001LTF fastq reads ENCSR000CEH ChIP-seq UBERON:0000955 brain tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 30 single-ended 280421271 Bing Ren, UCSD 9b0813bea40144999f4aba6f2f2b10e2 https://www.encodeproject.org/files/ENCFF001LTF/@@download/ENCFF001LTF.fastq.gz Illumina Genome Analyzer II /files/ENCFF786ODW/ released moderate library complexity, mild to moderate bottlenecking, inconsistent control read length, inconsistent platforms insufficient read depth, insufficient read length extremely low read depth ENCFF001LTG fastq reads ENCSR000CEH ChIP-seq UBERON:0000955 brain tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 30 single-ended 737402777 Bing Ren, UCSD dbf811d844e64ec9d460b0bdaa25abac https://www.encodeproject.org/files/ENCFF001LTG/@@download/ENCFF001LTG.fastq.gz Illumina HiSeq 2000 /files/ENCFF001LAO/ released moderate library complexity, mild to moderate bottlenecking, inconsistent platforms insufficient read depth, insufficient read length extremely low read depth ENCFF001NUY fastq reads 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 1 36 single-ended 721187461 Michael Snyder, Stanford 8e58d34984e462f782f7334eadce110a https://www.encodeproject.org/files/ENCFF001NUY/@@download/ENCFF001NUY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTS/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NVA fastq reads 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 2 1 36 single-ended 747614593 Michael Snyder, Stanford bdb3d4e602ca12892be793f30df605f0 https://www.encodeproject.org/files/ENCFF001NVA/@@download/ENCFF001NVA.fastq.gz Illumina Genome Analyzer /files/ENCFF001NTU/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OAO fastq reads 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 1 36 single-ended 1158858570 Michael Snyder, Stanford 706d63c2935991b192dcf5aa4f1caf6e https://www.encodeproject.org/files/ENCFF001OAO/@@download/ENCFF001OAO.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001OAR fastq reads ENCSR000ETF ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF2-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 938018403 Michael Snyder, Stanford f0bb1e61477a2fd98ded691b5f331688 https://www.encodeproject.org/files/ENCFF001OAR/@@download/ENCFF001OAR.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF302OTZ fastq reads ENCSR293WTN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 738913403 Michael Snyder, Stanford 2a2f835186cc379faa817dcd5e0e1865 https://www.encodeproject.org/files/ENCFF302OTZ/@@download/ENCFF302OTZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF825QPA fastq reads ENCSR293WTN ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ELF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 618967114 Michael Snyder, Stanford c00d819464e6eacb244d08989c29c7ca https://www.encodeproject.org/files/ENCFF825QPA/@@download/ENCFF825QPA.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF001LSZ fastq reads ENCSR000CEA ChIP-seq UBERON:0002370 thymus tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 425888815 Bing Ren, UCSD d1b018b757a214337ac4996913b7685a https://www.encodeproject.org/files/ENCFF001LSZ/@@download/ENCFF001LSZ.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KYT/ released low read length, mild to moderate bottlenecking, moderate library complexity insufficient read depth, poor library complexity extremely low read depth ENCFF001LTA fastq reads ENCSR000CEA ChIP-seq UBERON:0002370 thymus tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 520739019 Bing Ren, UCSD 817d7f1cff4252648b207dc136fc92f2 https://www.encodeproject.org/files/ENCFF001LTA/@@download/ENCFF001LTA.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KYS/ released low read length, mild to moderate bottlenecking, moderate library complexity insufficient read depth, poor library complexity extremely low read depth ENCFF001LKS fastq reads ENCSR000CBS ChIP-seq UBERON:0000948 heart tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 845503911 Bing Ren, UCSD b7e2fcfb2b2523d3641b75070e736cf8 https://www.encodeproject.org/files/ENCFF001LKS/@@download/ENCFF001LKS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIL/ released low read length, mild to moderate bottlenecking insufficient read depth ENCFF001LKT fastq reads ENCSR000CBS ChIP-seq UBERON:0000948 heart tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 728662005 Bing Ren, UCSD 40dd2bd766b5eeb75df37524dfc50523 https://www.encodeproject.org/files/ENCFF001LKT/@@download/ENCFF001LKT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIM/ released low read length, mild to moderate bottlenecking insufficient read depth ENCFF001NLK fastq reads ENCSR000EQX ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus UBTF-mouse DNA see document see document False 2012-06-15 ENCODE 1 1 36 single-ended 1021375159 Michael Snyder, Stanford 348d49e822c6a54a6b3c1bd3700b638a https://www.encodeproject.org/files/ENCFF001NLK/@@download/ENCFF001NLK.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001NLM fastq reads ENCSR000EQX ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus UBTF-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 889330379 Michael Snyder, Stanford 3a304a6402dd1b942b81988544f7bde8 https://www.encodeproject.org/files/ENCFF001NLM/@@download/ENCFF001NLM.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001LKP fastq reads ENCSR000CCA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 770333272 Bing Ren, UCSD a4866a732881075af92fe32429c7da6f https://www.encodeproject.org/files/ENCFF001LKP/@@download/ENCFF001LKP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIM/ released low read length insufficient read depth ENCFF001LKQ fastq reads ENCSR000CCA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 803225213 Bing Ren, UCSD 8eacc5eda2283503d19f23dd3d1e7394 https://www.encodeproject.org/files/ENCFF001LKQ/@@download/ENCFF001LKQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KIL/ released low read length insufficient read depth ENCFF001NOC fastq reads ENCSR000ERW ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 793182833 Michael Snyder, Stanford 95a7ee14869770f5f57c6549e3ccb241 https://www.encodeproject.org/files/ENCFF001NOC/@@download/ENCFF001NOC.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNN/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001NOF fastq reads ENCSR000ERW ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1587495011 Michael Snyder, Stanford 22ba6b9467c39be6117b42805a2891ca https://www.encodeproject.org/files/ENCFF001NOF/@@download/ENCFF001NOF.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNP/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms biological replicates with identical biosample ENCFF001LSK fastq reads ENCSR000CEG ChIP-seq UBERON:0000473 testis tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 827841808 Bing Ren, UCSD e508cb94c1508ad0036d8d9767ff4590 https://www.encodeproject.org/files/ENCFF001LSK/@@download/ENCFF001LSK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KXE/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001LSN fastq reads ENCSR000CEG ChIP-seq UBERON:0000473 testis tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1108138658 Bing Ren, UCSD 92087c74e50a02f293e09177a1c8c427 https://www.encodeproject.org/files/ENCFF001LSN/@@download/ENCFF001LSN.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KXN/ released low read length, low read depth, moderate library complexity, mild to moderate bottlenecking, inconsistent platforms ENCFF001LGH fastq reads ENCSR000CBL ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 741545851 Bing Ren, UCSD 183aa93675447d7779c373e1da2378c7 https://www.encodeproject.org/files/ENCFF001LGH/@@download/ENCFF001LGH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001JYM/ released low read length insufficient read depth ENCFF001LGI fastq reads ENCSR000CBL ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 1453014793 Bing Ren, UCSD 62dd21da575725327cd70ede798149c9 https://www.encodeproject.org/files/ENCFF001LGI/@@download/ENCFF001LGI.fastq.gz Illumina Genome Analyzer II /files/ENCFF001JYN/ released low read length insufficient read depth ENCFF001LHI fastq reads 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 1 36 single-ended 931311629 Bing Ren, UCSD 2da0411c22b9393055d1d41ffb68de45 https://www.encodeproject.org/files/ENCFF001LHI/@@download/ENCFF001LHI.fastq.gz Illumina HiSeq 2000 /files/ENCFF001JZL/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent control read length, borderline replicate concordance ENCFF001LHL fastq reads ENCSR000CFK ChIP-seq CL:0002476 bone marrow macrophage primary cell Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1614279285 Bing Ren, UCSD f439aa5b05e0aca8762219fe1fe1b77b https://www.encodeproject.org/files/ENCFF001LHL/@@download/ENCFF001LHL.fastq.gz Illumina HiSeq 2000 /files/ENCFF001JZE/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance ENCFF320KGQ fastq reads ENCSR150RGT ChIP-seq UBERON:0002028 hindbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1074085655 Richard Myers, HAIB 1e743e6524539c8817bb146ada8c2a98 SRA:SRR5111179 https://www.encodeproject.org/files/ENCFF320KGQ/@@download/ENCFF320KGQ.fastq.gz Illumina HiSeq 2000 /files/ENCFF787LKE/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF024MXS fastq reads ENCSR150RGT ChIP-seq UBERON:0002028 hindbrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1407393091 Richard Myers, HAIB 0fd358519919412a579bfc33a07c063e SRA:SRR5111178 https://www.encodeproject.org/files/ENCFF024MXS/@@download/ENCFF024MXS.fastq.gz Illumina HiSeq 2000 /files/ENCFF787LKE/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NJE fastq reads ENCSR000ERD ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NELFE-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 884769813 Michael Snyder, Stanford 48ffacbf3eabf41a5e245f70ad680215 https://www.encodeproject.org/files/ENCFF001NJE/@@download/ENCFF001NJE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF001NJG fastq reads ENCSR000ERD ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus NELFE-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 834214375 Michael Snyder, Stanford d46c6270ab6b8ca1b7a5a9ae3a760f6c https://www.encodeproject.org/files/ENCFF001NJG/@@download/ENCFF001NJG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth ENCFF042TOB fastq reads ENCSR777VNA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1 1 50 single-ended 1299857200 Richard Myers, HAIB a45959827f92b32f32c35f0de994e2e9 SRA:SRR5112068 https://www.encodeproject.org/files/ENCFF042TOB/@@download/ENCFF042TOB.fastq.gz Illumina HiSeq 2000 /files/ENCFF798MRO/ released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF299GTA fastq reads ENCSR777VNA ChIP-seq UBERON:0000948 heart tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 2 1 50 single-ended 982913959 Richard Myers, HAIB 5a1cc3646d8534b236e53acafb03dfde SRA:SRR5112069 https://www.encodeproject.org/files/ENCFF299GTA/@@download/ENCFF299GTA.fastq.gz Illumina HiSeq 2000 /files/ENCFF314WCC/ released low read depth, antibody characterized with exemption biological replicates with identical biosample ENCFF001LPN fastq reads ENCSR000CFI ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1770770669 Bing Ren, UCSD e90e9e4a761b33e80d57885159d92fe0 https://www.encodeproject.org/files/ENCFF001LPN/@@download/ENCFF001LPN.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KRK/ released low read length, mild to moderate bottlenecking insufficient read depth, poor library complexity ENCFF001LPR fastq reads 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 1 36 single-ended 2228558413 Bing Ren, UCSD 7f389b33cd3086d7ed3872cc70101686 https://www.encodeproject.org/files/ENCFF001LPR/@@download/ENCFF001LPR.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KRJ/ released low read length, mild to moderate bottlenecking insufficient read depth, poor library complexity ENCFF001NIZ fastq reads ENCSR000ERL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAX-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1080831141 Michael Snyder, Stanford ca7c170fba23a32445ce86d1ae6abc75 https://www.encodeproject.org/files/ENCFF001NIZ/@@download/ENCFF001NIZ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF001NJD fastq reads ENCSR000ERL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MAX-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1543164986 Michael Snyder, Stanford a4c2352361c67e5c5360977efbc2bd56 https://www.encodeproject.org/files/ENCFF001NJD/@@download/ENCFF001NJD.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length ENCFF880XUQ fastq reads ENCSR349JDH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 775223496 Michael Snyder, Stanford 8bd913addcb569e114dfeff805d5e49f https://www.encodeproject.org/files/ENCFF880XUQ/@@download/ENCFF880XUQ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF432YTR fastq reads ENCSR349JDH ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus TCF12-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 802732122 Michael Snyder, Stanford c2ea64b7a23d2d25fab9e701764853ba https://www.encodeproject.org/files/ENCFF432YTR/@@download/ENCFF432YTR.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF001NVG fastq reads 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 1 36 single-ended 931761169 Michael Snyder, Stanford b0c29d913d0edb92ae228b7efeeaafb7 https://www.encodeproject.org/files/ENCFF001NVG/@@download/ENCFF001NVG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance biological replicates with identical biosample ENCFF001NVI fastq reads ENCSR000ETK ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MAFK-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1226745149 Michael Snyder, Stanford d75ce2802a781b3a30a1d7ec7515c88d https://www.encodeproject.org/files/ENCFF001NVI/@@download/ENCFF001NVI.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance biological replicates with identical biosample ENCFF001NWP fastq reads 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 1 36 single-ended 959806526 Michael Snyder, Stanford 535fa6b9be802725d921f58c1edbb009 https://www.encodeproject.org/files/ENCFF001NWP/@@download/ENCFF001NWP.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms biological replicates with identical biosample ENCFF001NWR fastq reads ENCSR000ESK ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus GABPA-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 955206279 Michael Snyder, Stanford 1cf41c7f7a56a7ba9e4e4de85f9e321a https://www.encodeproject.org/files/ENCFF001NWR/@@download/ENCFF001NWR.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms biological replicates with identical biosample ENCFF929ZQW fastq reads ENCSR743ZJL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus IRF4-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 796430566 Michael Snyder, Stanford 677ef1046fabe4bef30235ce73d8c480 https://www.encodeproject.org/files/ENCFF929ZQW/@@download/ENCFF929ZQW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF190NEX fastq reads ENCSR743ZJL ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus IRF4-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 777982600 Michael Snyder, Stanford 6ad306f5a7e001cd287712bdf6290d2e https://www.encodeproject.org/files/ENCFF190NEX/@@download/ENCFF190NEX.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF464DYI fastq reads ENCSR491NUM ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 924778484 Richard Myers, HAIB 11c2a22b1dbdc7db05f4c2c7b993ffb4 SRA:SRR5111671 https://www.encodeproject.org/files/ENCFF464DYI/@@download/ENCFF464DYI.fastq.gz Illumina HiSeq 2000 /files/ENCFF637HTW/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF310VOQ fastq reads ENCSR491NUM ChIP-seq UBERON:0000948 heart tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 934347819 Richard Myers, HAIB 7f34d08dad0c3949dbb84ab77a7c94e8 SRA:SRR5111672 https://www.encodeproject.org/files/ENCFF310VOQ/@@download/ENCFF310VOQ.fastq.gz Illumina HiSeq 2000 /files/ENCFF637HTW/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001LGV fastq reads 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 1 36 single-ended 1013826871 Bing Ren, UCSD bcd517a44116067870cd1a8db2fb3970 https://www.encodeproject.org/files/ENCFF001LGV/@@download/ENCFF001LGV.fastq.gz Illumina HiSeq 2000 /files/ENCFF001JZL/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent control read length, moderate library complexity ENCFF001LGW fastq reads ENCSR000CFJ ChIP-seq CL:0002476 bone marrow macrophage primary cell Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1252220304 Bing Ren, UCSD 12469c44c8aef2fbd876da70ba51a920 https://www.encodeproject.org/files/ENCFF001LGW/@@download/ENCFF001LGW.fastq.gz Illumina HiSeq 2000 /files/ENCFF001JZE/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001LKY fastq reads ENCSR000CBJ ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 33 single-ended 681016013 Bing Ren, UCSD 2780f6fda36487aa0346e577ded037c3 https://www.encodeproject.org/files/ENCFF001LKY/@@download/ENCFF001LKY.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KKE/ released mild to moderate bottlenecking, mixed read lengths, inconsistent control read length, low read length, low read depth, moderate library complexity insufficient read depth, insufficient read length ENCFF001LLE fastq reads ENCSR000CBJ ChIP-seq UBERON:0002113 kidney tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 787401900 Bing Ren, UCSD 31830bc0a816bba4b559f047f8207dfc https://www.encodeproject.org/files/ENCFF001LLE/@@download/ENCFF001LLE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KKF/ released low read length, low read depth, mild to moderate bottlenecking, mixed read lengths, moderate library complexity insufficient read depth, insufficient read length ENCFF001MRN fastq reads 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 1 36 single-ended 551834958 Ross Hardison, PennState 270a7ff3d4c265fbf436b644ebd66b3b https://www.encodeproject.org/files/ENCFF001MRN/@@download/ENCFF001MRN.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSM/ released low read length, low read depth, mixed read lengths, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001MRQ fastq reads 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 2 1 41 single-ended 453798372 Ross Hardison, PennState 4c8898b087a582a4a43399e43b4e1c3f https://www.encodeproject.org/files/ENCFF001MRQ/@@download/ENCFF001MRQ.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MSW/ released low read length, low read depth, mixed read lengths, inconsistent control read length, inconsistent platforms biological replicates with identical biosample insufficient read depth ENCFF001LOI fastq reads ENCSR000CBW ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 649652575 Bing Ren, UCSD cb88968f80b51bba208252174b3b589e https://www.encodeproject.org/files/ENCFF001LOI/@@download/ENCFF001LOI.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KPS/ released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth ENCFF001LOK fastq reads ENCSR000CBW ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 905969306 Bing Ren, UCSD 34e72055a6a1a355cad06ab2d83480b7 https://www.encodeproject.org/files/ENCFF001LOK/@@download/ENCFF001LOK.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KPR/ released low read length, mild to moderate bottlenecking, borderline replicate concordance, moderate library complexity insufficient read depth ENCFF001NRT fastq reads 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 1 36 single-ended 1140546705 Michael Snyder, Stanford 85ad30a02746948a0411a69228db9823 https://www.encodeproject.org/files/ENCFF001NRT/@@download/ENCFF001NRT.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms biological replicates with identical biosample ENCFF001NRW fastq reads ENCSR000ETB ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ETS1-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 807877562 Michael Snyder, Stanford 1c41df0cebeb2296bccf6e5c6570207d https://www.encodeproject.org/files/ENCFF001NRW/@@download/ENCFF001NRW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms biological replicates with identical biosample ENCFF001NMY fastq reads ENCSR000EQP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZMIZ1-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 789170204 Michael Snyder, Stanford 6474968bb588670c94c5f0113a446b58 https://www.encodeproject.org/files/ENCFF001NMY/@@download/ENCFF001NMY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF001NNA fastq reads ENCSR000EQP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus ZMIZ1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1053191117 Michael Snyder, Stanford f79ffa893be8f82d5bda0ab080e71c98 https://www.encodeproject.org/files/ENCFF001NNA/@@download/ENCFF001NNA.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF654AKM fastq reads ENCSR973SOG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 666784504 Michael Snyder, Stanford 071078533b597fe19dde57d894eefe5d https://www.encodeproject.org/files/ENCFF654AKM/@@download/ENCFF654AKM.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF125CLY fastq reads ENCSR973SOG ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 625024634 Michael Snyder, Stanford 4196967234d2ae7911797d9ca50fcd08 https://www.encodeproject.org/files/ENCFF125CLY/@@download/ENCFF125CLY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms experiment not submitted to GEO ENCFF001NHI fastq reads ENCSR000EQR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 1053336778 Michael Snyder, Stanford 3863d0399302d94f8d2c9619d7fe6891 https://www.encodeproject.org/files/ENCFF001NHI/@@download/ENCFF001NHI.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF001NHK fastq reads ENCSR000EQR ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus HCFC1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1052341181 Michael Snyder, Stanford 38f155522e83813bd635214cd1c2d0b8 https://www.encodeproject.org/files/ENCFF001NHK/@@download/ENCFF001NHK.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms ENCFF001NGE fastq reads ENCSR000ERM ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 804002258 Michael Snyder, Stanford 272ab82012b2eb959a176cfce71c108d https://www.encodeproject.org/files/ENCFF001NGE/@@download/ENCFF001NGE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NGG fastq reads ENCSR000ERM ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 858847445 Michael Snyder, Stanford d35ff42974e72d764fc99ccf2755359e https://www.encodeproject.org/files/ENCFF001NGG/@@download/ENCFF001NGG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NQA fastq reads 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 1 36 single-ended 716368501 Michael Snyder, Stanford 64976867f5b72a18ed1c682f95d2f190 https://www.encodeproject.org/files/ENCFF001NQA/@@download/ENCFF001NQA.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NQG fastq reads ENCSR000ETR ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MYB-mouse DNA see document see document False 2011-02-07 ENCODE 2 1 36 single-ended 829109806 Michael Snyder, Stanford 69f482d3dcce968145159c3aeaf8440e https://www.encodeproject.org/files/ENCFF001NQG/@@download/ENCFF001NQG.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NYA fastq reads ENCSR000ETV ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus EP300-mouse DNA see document see document False 2011-02-07 ENCODE 2 1 36 single-ended 968478204 Michael Snyder, Stanford 7840bcc97bc1c553da07d0d5d58daf59 https://www.encodeproject.org/files/ENCFF001NYA/@@download/ENCFF001NYA.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NYE fastq reads 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 1 36 single-ended 1652369687 Michael Snyder, Stanford e0b40aba30f2ac2010d4aa9ceaae744b https://www.encodeproject.org/files/ENCFF001NYE/@@download/ENCFF001NYE.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NFV fastq reads ENCSR000EQZ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RCOR1-mouse DNA see document see document False 2012-06-15 ENCODE 1 1 36 single-ended 922302704 Michael Snyder, Stanford 2a124aca27e619a187404707ed92bb80 https://www.encodeproject.org/files/ENCFF001NFV/@@download/ENCFF001NFV.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms ENCFF001NFX fastq reads ENCSR000EQZ ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus RCOR1-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 1231369423 Michael Snyder, Stanford 7f3be493716f27ba97d767dfdbaa0e74 https://www.encodeproject.org/files/ENCFF001NFX/@@download/ENCFF001NFX.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance, inconsistent platforms ENCFF001NHM fastq reads ENCSR000ERU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus E2F4-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 876700294 Michael Snyder, Stanford a93447b896a8ccf35f75010b2e382cf8 https://www.encodeproject.org/files/ENCFF001NHM/@@download/ENCFF001NHM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth insufficient replicate concordance ENCFF001NHQ fastq reads ENCSR000ERU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus E2F4-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 1137497571 Michael Snyder, Stanford 75a37eed97475482f310dcb11483a96d https://www.encodeproject.org/files/ENCFF001NHQ/@@download/ENCFF001NHQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth insufficient replicate concordance ENCFF001OAX fastq reads 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 1 36 single-ended 922940872 Michael Snyder, Stanford 86e1b41f014b98b182e03c430bf545ac https://www.encodeproject.org/files/ENCFF001OAX/@@download/ENCFF001OAX.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OAZ fastq reads ENCSR000ESF ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZC3H11A-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 985534876 Michael Snyder, Stanford b76237984bfd5538c066998590046e0d https://www.encodeproject.org/files/ENCFF001OAZ/@@download/ENCFF001OAZ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NEO fastq reads ENCSR000ERC ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus BHLHE40-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 988831705 Michael Snyder, Stanford 9d40dd4db8c3a312691a1d26a5226d29 https://www.encodeproject.org/files/ENCFF001NEO/@@download/ENCFF001NEO.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking duplicate lane review ENCFF001NEQ fastq reads ENCSR000ERC ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus BHLHE40-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1300337811 Michael Snyder, Stanford 63c971b703b9f2b0870a2cd01fa85063 https://www.encodeproject.org/files/ENCFF001NEQ/@@download/ENCFF001NEQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking duplicate lane review ENCFF001NEW fastq reads ENCSR000EQV ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD1-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 982781920 Michael Snyder, Stanford 471b11377370328fa8611fcb4eb7267d https://www.encodeproject.org/files/ENCFF001NEW/@@download/ENCFF001NEW.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms ENCFF001NEY fastq reads ENCSR000EQV ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CHD1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 838855592 Michael Snyder, Stanford 8d045b4d6f721da922941f106dd97aaa https://www.encodeproject.org/files/ENCFF001NEY/@@download/ENCFF001NEY.fastq.gz Illumina Genome Analyzer /files/ENCFF001NIM/ released low read length, low read depth, inconsistent platforms ENCFF996MWJ fastq reads ENCSR705HGT ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 1 1 36 single-ended 591216480 Michael Snyder, Stanford 3987c43c487558b8920afee429b62517 https://www.encodeproject.org/files/ENCFF996MWJ/@@download/ENCFF996MWJ.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF550MZG fastq reads ENCSR705HGT ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus USF1-mouse DNA False 2014-12-08 ENCODE 2 1 36 single-ended 854969794 Michael Snyder, Stanford d464f0e8c09eb281eb356342fcb29920 https://www.encodeproject.org/files/ENCFF550MZG/@@download/ENCFF550MZG.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity, inconsistent platforms experiment not submitted to GEO, biological replicates with identical biosample ENCFF001NYM fastq reads 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 1 36 single-ended 869695303 Michael Snyder, Stanford 4f84eda57d556e64db566a5afaf98e97 https://www.encodeproject.org/files/ENCFF001NYM/@@download/ENCFF001NYM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NYQ fastq reads ENCSR000ETM ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus POLR2AphosphoS2-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 969057436 Michael Snyder, Stanford 76c15821a69d07fd9835b05603498917 https://www.encodeproject.org/files/ENCFF001NYQ/@@download/ENCFF001NYQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth biological replicates with identical biosample ENCFF001NXH fastq reads 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 1 36 single-ended 858689441 Michael Snyder, Stanford 385d7609c8d1d408b527788dd1923f63 https://www.encodeproject.org/files/ENCFF001NXH/@@download/ENCFF001NXH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NXM fastq reads ENCSR000ETP ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus EP300-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1063047092 Michael Snyder, Stanford 194e6ba808b821b58a733bf1919b6bff https://www.encodeproject.org/files/ENCFF001NXM/@@download/ENCFF001NXM.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking biological replicates with identical biosample ENCFF001NQP fastq reads 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 1 36 single-ended 1005318875 Michael Snyder, Stanford 03a3d5e2998fde6495967e9e7b800c38 https://www.encodeproject.org/files/ENCFF001NQP/@@download/ENCFF001NQP.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001NQQ fastq reads ENCSR000EUA ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus MYC-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1107674500 Michael Snyder, Stanford 2500b9ce365596e7a8f4c32ef609594a https://www.encodeproject.org/files/ENCFF001NQQ/@@download/ENCFF001NQQ.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity biological replicates with identical biosample ENCFF001MLF fastq reads ENCSR000DIU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 1 1 36 single-ended 607480699 Ross Hardison, PennState 13cb55536563e2f404ef8356ca31096c https://www.encodeproject.org/files/ENCFF001MLF/@@download/ENCFF001MLF.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MLS/ released low read length, low read depth, inconsistent platforms ENCFF001MLG fastq reads ENCSR000DIU ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus CTCF-mouse DNA see document see document False 2012-02-13 ENCODE 2 1 36 single-ended 806190305 Ross Hardison, PennState cb106f71623b64b241c3bf8647d34d52 https://www.encodeproject.org/files/ENCFF001MLG/@@download/ENCFF001MLG.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001MLY/ released low read length, low read depth, inconsistent control read length, inconsistent platforms ENCFF001NPB fastq reads 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 1 36 single-ended 764843245 Michael Snyder, Stanford 902e7f1b9aea32b694d088e304ffbbe4 https://www.encodeproject.org/files/ENCFF001NPB/@@download/ENCFF001NPB.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NPD fastq reads ENCSR000ESN ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus CHD1-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 888145478 Michael Snyder, Stanford e1040dcdbdd306a5be3c414bd9de63e9 https://www.encodeproject.org/files/ENCFF001NPD/@@download/ENCFF001NPD.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OBN fastq reads 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 1 36 single-ended 953129401 Michael Snyder, Stanford d699cf94e6f73821a224315e846bffa4 https://www.encodeproject.org/files/ENCFF001OBN/@@download/ENCFF001OBN.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001OBP fastq reads ENCSR000ESD ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 882995364 Michael Snyder, Stanford f139950cc385e8ac957c82cbd2b98b55 https://www.encodeproject.org/files/ENCFF001OBP/@@download/ENCFF001OBP.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms biological replicates with identical biosample ENCFF001NOK fastq reads ENCSR000ERV ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 1 1 36 single-ended 756106339 Michael Snyder, Stanford 2c1160b93363252494e830a43d75a2c8 https://www.encodeproject.org/files/ENCFF001NOK/@@download/ENCFF001NOK.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNN/ released low read length, low read depth, inconsistent platforms biological replicates with identical biosample ENCFF001NON fastq reads ENCSR000ERV ChIP-seq EFO:0007075 ES-E14 stem cell Mus musculus ZNF384-mouse DNA see document see document False 2012-08-16 ENCODE 2 1 36 single-ended 1423653479 Michael Snyder, Stanford 9723a6dd2f002b60b5f96be9341ca2b8 https://www.encodeproject.org/files/ENCFF001NON/@@download/ENCFF001NON.fastq.gz Illumina Genome Analyzer /files/ENCFF001NNP/ released low read length, low read depth, inconsistent platforms biological replicates with identical biosample ENCFF938GAS fastq reads ENCSR765RPR ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1 1 50 single-ended 1869515221 Richard Myers, HAIB 4c697252bab23245ab23f30cfbf01518 SRA:SRR5112038 https://www.encodeproject.org/files/ENCFF938GAS/@@download/ENCFF938GAS.fastq.gz Illumina HiSeq 2000 /files/ENCFF747FRP/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF548JVO fastq reads ENCSR765RPR ChIP-seq UBERON:0002107 liver tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 2 1 50 single-ended 1093521687 Richard Myers, HAIB 8b49d49f43d8bebb16ed38b91459a1a7 SRA:SRR5112039 https://www.encodeproject.org/files/ENCFF548JVO/@@download/ENCFF548JVO.fastq.gz Illumina HiSeq 2000 /files/ENCFF747FRP/ released low read depth, mild to moderate bottlenecking, antibody characterized with exemption biological replicates with identical biosample ENCFF671VKD fastq reads ENCSR450KVW ChIP-seq UBERON:0000945 stomach tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 2 1 50 single-ended 1200033178 Richard Myers, HAIB 24fd908cdf923a562145a19996f09203 SRA:SRR5111591 https://www.encodeproject.org/files/ENCFF671VKD/@@download/ENCFF671VKD.fastq.gz Illumina HiSeq 2000 /files/ENCFF172HFY/ released antibody characterized with exemption biological replicates with identical biosample ENCFF682HTS fastq reads ENCSR450KVW ChIP-seq UBERON:0000945 stomach tissue Mus musculus EP300-mouse DNA False 2016-05-17 ENCODE 1 1 50 single-ended 1094098855 Richard Myers, HAIB 75a7dc10b54e80bb12b6cfe54656c72b SRA:SRR5111590 https://www.encodeproject.org/files/ENCFF682HTS/@@download/ENCFF682HTS.fastq.gz Illumina HiSeq 2000 /files/ENCFF329PLP/ released antibody characterized with exemption biological replicates with identical biosample ENCFF229RMI fastq reads ENCSR041SMK ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1176592691 Richard Myers, HAIB aa66cc22ac82d161ed420256e9db1eb6 SRA:SRR5112437 https://www.encodeproject.org/files/ENCFF229RMI/@@download/ENCFF229RMI.fastq.gz Illumina HiSeq 2000 /files/ENCFF299JNL/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF978BAW fastq reads ENCSR041SMK ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1113492994 Richard Myers, HAIB 749b740df71ae9787b8a95ef33638c2c SRA:SRR5112438 https://www.encodeproject.org/files/ENCFF978BAW/@@download/ENCFF978BAW.fastq.gz Illumina HiSeq 2000 /files/ENCFF299JNL/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NLV fastq reads ENCSR000ERP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TBP-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 911002490 Michael Snyder, Stanford 371e8f7219f38236fef86f25caa494d4 https://www.encodeproject.org/files/ENCFF001NLV/@@download/ENCFF001NLV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth ENCFF001NLX fastq reads ENCSR000ERP ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus TBP-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 889716228 Michael Snyder, Stanford 17b1fadacffa05627612b33aa1a25391 https://www.encodeproject.org/files/ENCFF001NLX/@@download/ENCFF001NLX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIF/ released low read length, low read depth ENCFF538QDO fastq reads ENCSR677HXC ChIP-seq UBERON:0001890 forebrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 1 1 50 single-ended 1221837046 Richard Myers, HAIB f1d4eaf0677dcf81cdfac526e10db8dc SRA:SRR5111961 https://www.encodeproject.org/files/ENCFF538QDO/@@download/ENCFF538QDO.fastq.gz Illumina HiSeq 2000 /files/ENCFF184PEP/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF712ARW fastq reads ENCSR677HXC ChIP-seq UBERON:0001890 forebrain tissue Mus musculus CTCF-mouse DNA False 2016-05-18 ENCODE 2 1 50 single-ended 1068880582 Richard Myers, HAIB ba2d0bdce5ab479324301da227ab8e76 SRA:SRR5111960 https://www.encodeproject.org/files/ENCFF712ARW/@@download/ENCFF712ARW.fastq.gz Illumina HiSeq 2000 /files/ENCFF184PEP/ released low read depth, antibody characterized with exemption NTR biosample, biological replicates with identical biosample ENCFF001NZD fastq reads 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 1 36 single-ended 1161825548 Michael Snyder, Stanford f844cadbcc81f97e4d8edb4ef1565a60 https://www.encodeproject.org/files/ENCFF001NZD/@@download/ENCFF001NZD.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, inconsistent platforms biological replicates with identical biosample ENCFF001NZF fastq reads ENCSR000ETC ChIP-seq EFO:0003971 MEL cell line cell line Mus musculus SIN3A-mouse DNA see document see document False 2012-06-15 ENCODE 2 1 36 single-ended 1249507627 Michael Snyder, Stanford ce14824798f3af559c6f76f53166ae0e https://www.encodeproject.org/files/ENCFF001NZF/@@download/ENCFF001NZF.fastq.gz Illumina Genome Analyzer /files/ENCFF001NCF/, /files/ENCFF001NCH/ released low read length, inconsistent platforms biological replicates with identical biosample ENCFF001NJR fastq reads ENCSR000ERE ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MXI1-mouse DNA see document see document False 2011-09-19 ENCODE 1 1 36 single-ended 916929123 Michael Snyder, Stanford ba0583a44ecc855561a5cbfa5b05b976 https://www.encodeproject.org/files/ENCFF001NJR/@@download/ENCFF001NJR.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001NJU fastq reads ENCSR000ERE ChIP-seq EFO:0005233 CH12.LX cell line Mus musculus MXI1-mouse DNA see document see document False 2011-09-19 ENCODE 2 1 36 single-ended 1025607393 Michael Snyder, Stanford 6fa596c4a79f72dce31c82f2569d4c8b https://www.encodeproject.org/files/ENCFF001NJU/@@download/ENCFF001NJU.fastq.gz Illumina Genome Analyzer II /files/ENCFF001NIM/ released low read length, low read depth, mild to moderate bottlenecking ENCFF001LMV fastq reads ENCSR000CBU ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 873415933 Bing Ren, UCSD 97c751e2bffc3ab4e4321282863e9c86 https://www.encodeproject.org/files/ENCFF001LMV/@@download/ENCFF001LMV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KNY/ released low read length, low read depth, mild to moderate bottlenecking insufficient read depth ENCFF001LMX fastq reads ENCSR000CBU ChIP-seq UBERON:0002107 liver tissue Mus musculus CTCF-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 831603429 Bing Ren, UCSD 2997f0b24bdcac54ec02ac864f1d8f4b https://www.encodeproject.org/files/ENCFF001LMX/@@download/ENCFF001LMX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KNX/ released low read length, low read depth, mild to moderate bottlenecking insufficient read depth ENCFF001LNH fastq reads ENCSR000CBR ChIP-seq UBERON:0002107 liver tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 223741018 Bing Ren, UCSD 4fcc668a15d21b45fab047dab977bc59 https://www.encodeproject.org/files/ENCFF001LNH/@@download/ENCFF001LNH.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KNX/ released low read length insufficient read depth extremely low read depth ENCFF001LNR fastq reads ENCSR000CBR ChIP-seq UBERON:0002107 liver tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 798813652 Bing Ren, UCSD 3e603700018dc39c68627061a97aa983 https://www.encodeproject.org/files/ENCFF001LNR/@@download/ENCFF001LNR.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KNY/ released low read length insufficient read depth extremely low read depth ENCFF001LRL fastq reads ENCSR000CBZ ChIP-seq UBERON:0002106 spleen tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 721564026 Bing Ren, UCSD 5d1b072b37202b54981ad287aa7c7d8c https://www.encodeproject.org/files/ENCFF001LRL/@@download/ENCFF001LRL.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KVR/ released low read length, low read depth, inconsistent platforms ENCFF001LRT fastq reads ENCSR000CBZ ChIP-seq UBERON:0002106 spleen tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 819053704 Bing Ren, UCSD a11847b3c696956d09a162cdf20aeb09 https://www.encodeproject.org/files/ENCFF001LRT/@@download/ENCFF001LRT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KWE/ released low read length, low read depth, inconsistent control read length, inconsistent platforms ENCFF001LRW fastq reads ENCSR000CEF ChIP-seq UBERON:0000473 testis tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 417563407 Bing Ren, UCSD 27d8add215abcec656bc1c4693839ffc https://www.encodeproject.org/files/ENCFF001LRW/@@download/ENCFF001LRW.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KXN/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms insufficient read depth, insufficient replicate concordance ENCFF001LRX fastq reads ENCSR000CEF ChIP-seq UBERON:0000473 testis tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 823221182 Bing Ren, UCSD 95cb223c7b394648881cb9f534817b72 https://www.encodeproject.org/files/ENCFF001LRX/@@download/ENCFF001LRX.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KXE/ released low read length, low read depth, mild to moderate bottlenecking, inconsistent platforms insufficient read depth, insufficient replicate concordance ENCFF001LGS fastq reads ENCSR000CBM ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 726466319 Bing Ren, UCSD a9aa109d830884bf1939687de7cc0597 https://www.encodeproject.org/files/ENCFF001LGS/@@download/ENCFF001LGS.fastq.gz Illumina Genome Analyzer II /files/ENCFF001JYN/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance insufficient read depth ENCFF001LGT fastq reads ENCSR000CBM ChIP-seq UBERON:0002371 bone marrow tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 984688995 Bing Ren, UCSD 5cfd5849fd51d13dd45158718c9a146a https://www.encodeproject.org/files/ENCFF001LGT/@@download/ENCFF001LGT.fastq.gz Illumina Genome Analyzer II /files/ENCFF001JYM/ released low read length, low read depth, mild to moderate bottlenecking, borderline replicate concordance insufficient read depth ENCFF001LPM fastq reads ENCSR000CDX ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 359116018 Bing Ren, UCSD 97ccc3f41ae802b4224e9a3eea899cda https://www.encodeproject.org/files/ENCFF001LPM/@@download/ENCFF001LPM.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KSH/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity extremely low read depth ENCFF001LPS fastq reads ENCSR000CDX ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus CTCF-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 1220774328 Bing Ren, UCSD 7606703b05bbb6bbde0286b898ff08c4 https://www.encodeproject.org/files/ENCFF001LPS/@@download/ENCFF001LPS.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KSJ/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity extremely low read depth ENCFF001LQA fastq reads ENCSR000CDY ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 1 1 36 single-ended 405519061 Bing Ren, UCSD d0688acd2c24d09d038c54a983224a0e https://www.encodeproject.org/files/ENCFF001LQA/@@download/ENCFF001LQA.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KSH/ released low read length, mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF001LQF fastq reads ENCSR000CDY ChIP-seq UBERON:0002264 olfactory bulb tissue Mus musculus POLR2A-mouse DNA see document see document False 2012-04-13 ENCODE 2 1 36 single-ended 834938469 Bing Ren, UCSD 9ee80ebf60ff2ae3f5d4c281027613df https://www.encodeproject.org/files/ENCFF001LQF/@@download/ENCFF001LQF.fastq.gz Illumina HiSeq 2000 /files/ENCFF001KSJ/ released low read length, mild to moderate bottlenecking, moderate library complexity insufficient read depth ENCFF001LOV fastq reads ENCSR000CBX ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 1169795981 Bing Ren, UCSD 709589a6b7e4a99a81104f63e602d14d https://www.encodeproject.org/files/ENCFF001LOV/@@download/ENCFF001LOV.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001KPR/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001LOX fastq reads ENCSR000CBX ChIP-seq CL:2000042 embryonic fibroblast primary cell Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 1219413862 Bing Ren, UCSD d6ddb0323a9faeac7a5b85fc4cda51a1 https://www.encodeproject.org/files/ENCFF001LOX/@@download/ENCFF001LOX.fastq.gz Illumina Genome Analyzer IIx /files/ENCFF001KPS/ released low read length, low read depth, mild to moderate bottlenecking, moderate library complexity ENCFF001LIV fastq reads ENCSR000CBP ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 1 1 36 single-ended 857670263 Bing Ren, UCSD 51b80cb1f332091dfbbec78c834e211a https://www.encodeproject.org/files/ENCFF001LIV/@@download/ENCFF001LIV.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KCX/ released low read length, mild to moderate bottlenecking insufficient read depth extremely low read depth ENCFF001LIW fastq reads ENCSR000CBP ChIP-seq UBERON:0005343 cortical plate tissue Mus musculus POLR2A-mouse DNA see document see document False 2011-07-22 ENCODE 2 1 36 single-ended 904548028 Bing Ren, UCSD d6167997aa6af2471e51a9e66a26c951 https://www.encodeproject.org/files/ENCFF001LIW/@@download/ENCFF001LIW.fastq.gz Illumina Genome Analyzer II /files/ENCFF001KDF/ released low read length, mild to moderate bottlenecking insufficient read depth extremely low read depth