| generated_at: '2026-06-08T16:21:37.042878+00:00' |
| source_config: configs/k562_molecular_sources.yaml |
| assembly_target: hg19 |
| record_count: 29 |
| ok_count: 20 |
| failed_count: 0 |
| manual_count: 9 |
| records: |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: CNhs11250 |
| usage: promoter activity and target-gene expression/power covariates |
| validation_status: manual_required |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: CNhs12334 |
| usage: promoter activity and target-gene expression/power covariates |
| validation_status: manual_required |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: CNhs12335 |
| usage: promoter activity and target-gene expression/power covariates |
| validation_status: manual_required |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: CNhs12336 |
| usage: promoter activity and target-gene expression/power covariates |
| validation_status: manual_required |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg19.ctss.bed.gz |
| validation_status: url_ok |
| download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562.CNhs11250.10454-106G4.hg19.ctss.bed.gz |
| assembly: hg19 |
| file_format: bed |
| content_type: application/x-gzip |
| file_size: 14817958 |
| last_modified: Wed, 29 Jun 2011 10:40:06 GMT |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep1.CNhs12334.10824-111C5.hg19.ctss.bed.gz |
| validation_status: url_ok |
| download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep1.CNhs12334.10824-111C5.hg19.ctss.bed.gz |
| assembly: hg19 |
| file_format: bed |
| content_type: application/x-gzip |
| file_size: 9107710 |
| last_modified: Wed, 29 Jun 2011 12:53:42 GMT |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz |
| validation_status: url_ok |
| download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep2.CNhs12335.10825-111C6.hg19.ctss.bed.gz |
| assembly: hg19 |
| file_format: bed |
| content_type: application/x-gzip |
| file_size: 10122187 |
| last_modified: Wed, 29 Jun 2011 12:54:25 GMT |
| - family: cage |
| provider: FANTOM5 |
| biosample: K562 |
| assay: CAGE |
| identifier: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep3.CNhs12336.10826-111C7.hg19.ctss.bed.gz |
| validation_status: url_ok |
| download_url: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/basic/human.cell_line.hCAGE/chronic%2520myelogenous%2520leukemia%2520cell%2520line%253aK562%2520ENCODE%252c%2520biol_rep3.CNhs12336.10826-111C7.hg19.ctss.bed.gz |
| assembly: hg19 |
| file_format: bed |
| content_type: application/x-gzip |
| file_size: 11214315 |
| last_modified: Wed, 29 Jun 2011 12:55:15 GMT |
| - family: ctcf_cohesin |
| provider: ENCODE |
| biosample: K562 |
| assay: |
| - CTCF ChIP-seq |
| - RAD21 ChIP-seq |
| - SMC1A/SMC3 ChIP-seq |
| accession: ENCFF168IFW |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF168IFW/ |
| status: released |
| assembly: GRCh38 |
| file_format: bigWig |
| output_type: signal p-value |
| file_size: 427316411 |
| md5sum: 8f9feb5f030d25a4f2623e0404d63357 |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| dataset: /experiments/ENCSR000DWE/ |
| download_url: https://www.encodeproject.org/files/ENCFF168IFW/@@download/ENCFF168IFW.bigWig |
| s3_uri: s3://encode-public/2020/09/25/5f56d601-0bb6-4781-a8a0-76f3ad7d7d52/ENCFF168IFW.bigWig |
| - family: ctcf_cohesin |
| provider: ENCODE |
| biosample: K562 |
| assay: |
| - CTCF ChIP-seq |
| - RAD21 ChIP-seq |
| - SMC1A/SMC3 ChIP-seq |
| accession: ENCFF736NYC |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF736NYC/ |
| status: released |
| assembly: GRCh38 |
| file_format: bed |
| output_type: IDR thresholded peaks |
| file_size: 724170 |
| md5sum: 606e423b6ab856b7a61767838d21dbf8 |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| dataset: /experiments/ENCSR000DWE/ |
| download_url: https://www.encodeproject.org/files/ENCFF736NYC/@@download/ENCFF736NYC.bed.gz |
| s3_uri: s3://encode-public/2020/09/25/a988bfd0-11ca-4abf-8662-29f30dc09772/ENCFF736NYC.bed.gz |
| - family: ctcf_cohesin |
| provider: ENCODE |
| biosample: K562 |
| assay: |
| - CTCF ChIP-seq |
| - RAD21 ChIP-seq |
| - SMC1A/SMC3 ChIP-seq |
| accession: ENCFF330SHG |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF330SHG/ |
| status: released |
| assembly: GRCh38 |
| file_format: bed |
| output_type: IDR thresholded peaks |
| file_size: 935586 |
| md5sum: 356a9862fda97a5f8c636305ebd360c0 |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| dataset: /experiments/ENCSR942XQI/ |
| download_url: https://www.encodeproject.org/files/ENCFF330SHG/@@download/ENCFF330SHG.bed.gz |
| s3_uri: s3://encode-public/2022/08/24/f8806f91-014f-4244-9dd3-7d178df670ed/ENCFF330SHG.bed.gz |
| - family: ctcf_cohesin |
| provider: ENCODE |
| biosample: K562 |
| assay: |
| - CTCF ChIP-seq |
| - RAD21 ChIP-seq |
| - SMC1A/SMC3 ChIP-seq |
| accession: ENCFF355MNE |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF355MNE/ |
| status: released |
| assembly: GRCh38 |
| file_format: bed |
| output_type: conservative IDR thresholded peaks |
| file_size: 767024 |
| md5sum: eb5e6feb3e8862f026ba5b27e43eaec5 |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| dataset: /experiments/ENCSR388QZF/ |
| download_url: https://www.encodeproject.org/files/ENCFF355MNE/@@download/ENCFF355MNE.bed.gz |
| s3_uri: s3://encode-public/2020/11/27/93ca2939-f77a-41d7-a4a4-ffbad350dd95/ENCFF355MNE.bed.gz |
| - family: ctcf_cohesin |
| provider: ENCODE |
| biosample: K562 |
| assay: |
| - CTCF ChIP-seq |
| - RAD21 ChIP-seq |
| - SMC1A/SMC3 ChIP-seq |
| identifier: ENCODE search for K562 released bigWig/peak files |
| usage: boundary, loop, and TAD-context features after activity/contact features |
| are stable |
| validation_status: manual_required |
| - family: dnase |
| provider: ENCODE |
| biosample: K562 |
| assay: DNase-seq |
| accession: ENCFF827NRR |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF827NRR/ |
| status: archived |
| assembly: hg19 |
| file_format: bigWig |
| output_type: signal of unique reads |
| file_size: 168663469 |
| md5sum: c1787835e5e231d7cf2bc3387b2bf97a |
| biological_replicates: |
| - 1 |
| technical_replicates: |
| - '1_1' |
| dataset: /experiments/ENCSR101TGA/ |
| download_url: https://www.encodeproject.org/files/ENCFF827NRR/@@download/ENCFF827NRR.bigWig |
| s3_uri: s3://encode-public/2016/05/11/1367eb79-10ef-4fa0-ae79-66024926f6e5/ENCFF827NRR.bigWig |
| - family: dnase |
| provider: ENCODE |
| biosample: K562 |
| assay: DNase-seq |
| accession: ENCFF425WDA |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF425WDA/ |
| status: released |
| assembly: GRCh38 |
| file_format: bam |
| output_type: alignments |
| file_size: 798775645 |
| md5sum: 55077c1a250db3ed78d9c937d92dc86c |
| biological_replicates: |
| - 2 |
| technical_replicates: |
| - '2_1' |
| dataset: /experiments/ENCSR000EOT/ |
| download_url: https://www.encodeproject.org/files/ENCFF425WDA/@@download/ENCFF425WDA.bam |
| s3_uri: s3://encode-public/2020/11/18/c0cf66b0-28e0-44d3-9df1-0dc3789a1cb7/ENCFF425WDA.bam |
| - family: dnase |
| provider: ENCODE |
| biosample: K562 |
| assay: DNase-seq |
| accession: ENCFF205FNC |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF205FNC/ |
| status: released |
| assembly: GRCh38 |
| file_format: bam |
| output_type: alignments |
| file_size: 11870480765 |
| md5sum: 6b180efe8b376ebc57ae30e8c6bf37fb |
| biological_replicates: |
| - 1 |
| technical_replicates: |
| - '1_1' |
| - '1_2' |
| dataset: /experiments/ENCSR000EOT/ |
| download_url: https://www.encodeproject.org/files/ENCFF205FNC/@@download/ENCFF205FNC.bam |
| s3_uri: s3://encode-public/2020/11/18/62e44159-c267-4b15-a8ee-3d100fbf4418/ENCFF205FNC.bam |
| - family: dnase |
| provider: ENCODE |
| biosample: K562 |
| assay: DNase-seq |
| accession: ENCFF447GZO |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF447GZO/ |
| status: archived |
| assembly: hg19 |
| file_format: bigWig |
| output_type: signal of unique reads |
| file_size: 171310286 |
| md5sum: 6009f78f2bc6b21bfc03a9d5e78c6513 |
| biological_replicates: |
| - 1 |
| technical_replicates: |
| - '1_1' |
| dataset: /experiments/ENCSR945ENZ/ |
| download_url: https://www.encodeproject.org/files/ENCFF447GZO/@@download/ENCFF447GZO.bigWig |
| s3_uri: s3://encode-public/2016/05/11/86462f8e-6200-4c6e-9609-5eea74661242/ENCFF447GZO.bigWig |
| - family: external_e2g_predictions |
| provider: |
| - ABC |
| - ENCODE-rE2G |
| - gABC |
| biosample: null |
| assay: null |
| identifier: ABC |
| usage: external-score comparison on exact Seq2State candidates before retraining |
| validation_status: manual_required |
| - family: external_e2g_predictions |
| provider: |
| - ABC |
| - ENCODE-rE2G |
| - gABC |
| biosample: null |
| assay: null |
| identifier: ENCODE-rE2G |
| usage: external-score comparison on exact Seq2State candidates before retraining |
| validation_status: manual_required |
| - family: external_e2g_predictions |
| provider: |
| - ABC |
| - ENCODE-rE2G |
| - gABC |
| biosample: null |
| assay: null |
| identifier: gABC |
| usage: external-score comparison on exact Seq2State candidates before retraining |
| validation_status: manual_required |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| accession: ENCFF779QTH |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF779QTH/ |
| status: released |
| assembly: GRCh38 |
| file_format: bigWig |
| output_type: fold change over control |
| file_size: 236381149 |
| md5sum: 81aaf56e59eaa1c9742b5e0c8216860f |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| dataset: /experiments/ENCSR000AKP/ |
| download_url: https://www.encodeproject.org/files/ENCFF779QTH/@@download/ENCFF779QTH.bigWig |
| s3_uri: s3://encode-public/2016/08/12/2e25c3ae-0b4a-4155-8750-d959da5dbb5c/ENCFF779QTH.bigWig |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| accession: ENCFF544LXB |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF544LXB/ |
| status: released |
| assembly: GRCh38 |
| file_format: bed |
| output_type: pseudoreplicated peaks |
| file_size: 1455796 |
| md5sum: 81a2d09ef690a3317f6b0e793690cfdc |
| biological_replicates: |
| - 1 |
| - 2 |
| - 3 |
| technical_replicates: |
| - '1_1' |
| - '2_1' |
| - '3_1' |
| - '3_2' |
| dataset: /experiments/ENCSR000AKP/ |
| download_url: https://www.encodeproject.org/files/ENCFF544LXB/@@download/ENCFF544LXB.bed.gz |
| s3_uri: s3://encode-public/2022/06/14/77871d7d-ef0b-40da-8537-48dfd391bbdf/ENCFF544LXB.bed.gz |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| accession: ENCFF600THN |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF600THN/ |
| status: released |
| assembly: GRCh38 |
| file_format: bam |
| output_type: alignments |
| file_size: 465061663 |
| md5sum: d0cb34fd6b9f4b64fee14031d5f130e1 |
| biological_replicates: |
| - 1 |
| technical_replicates: |
| - '1_1' |
| dataset: /experiments/ENCSR000AKP/ |
| download_url: https://www.encodeproject.org/files/ENCFF600THN/@@download/ENCFF600THN.bam |
| s3_uri: s3://encode-public/2022/06/14/03e349f5-48f1-474f-812e-a1830ee6df4f/ENCFF600THN.bam |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| accession: ENCFF232RQF |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF232RQF/ |
| status: released |
| assembly: GRCh38 |
| file_format: bam |
| output_type: alignments |
| file_size: 2455019320 |
| md5sum: 60129abdf21c0cb86ee3b918e62e172c |
| biological_replicates: |
| - 3 |
| technical_replicates: |
| - '3_1' |
| - '3_2' |
| dataset: /experiments/ENCSR000AKP/ |
| download_url: https://www.encodeproject.org/files/ENCFF232RQF/@@download/ENCFF232RQF.bam |
| s3_uri: s3://encode-public/2022/06/14/f84f4ebb-3154-4a2b-8106-23360a30bd47/ENCFF232RQF.bam |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| accession: ENCFF704LGA |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF704LGA/ |
| status: released |
| assembly: GRCh38 |
| file_format: bam |
| output_type: alignments |
| file_size: 226787968 |
| md5sum: f58b860384aaeceebbb64f77df1dc837 |
| biological_replicates: |
| - 2 |
| technical_replicates: |
| - '2_1' |
| dataset: /experiments/ENCSR000AKP/ |
| download_url: https://www.encodeproject.org/files/ENCFF704LGA/@@download/ENCFF704LGA.bam |
| s3_uri: s3://encode-public/2022/06/14/47636cb3-e39f-4554-a8aa-fa7c22f3fc93/ENCFF704LGA.bam |
| - family: h3k27ac |
| provider: ENCODE |
| biosample: K562 |
| assay: H3K27ac ChIP-seq |
| identifier: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig |
| validation_status: url_ok |
| download_url: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig |
| assembly: hg19 |
| file_format: bigWig |
| content_type: null |
| file_size: 306678205 |
| last_modified: Fri, 28 Jan 2011 05:18:18 GMT |
| - family: reference_hic |
| provider: ENCODE |
| biosample: reference or K562-compatible |
| assay: Hi-C |
| accession: ENCFF621AIY |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF621AIY/ |
| status: released |
| assembly: GRCh38 |
| file_format: hic |
| output_type: mapping quality thresholded contact matrix |
| file_size: 33783625697 |
| md5sum: 71e5dc072beddbdcda11c9016696e142 |
| biological_replicates: |
| - 1 |
| - 2 |
| technical_replicates: |
| - '1_1' |
| - '1_2' |
| - '2_1' |
| - '2_2' |
| - '2_3' |
| - '2_5' |
| - '2_6' |
| dataset: /experiments/ENCSR479XDG/ |
| download_url: https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic |
| s3_uri: s3://encode-public/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic |
| - family: reference_hic |
| provider: ENCODE |
| biosample: reference or K562-compatible |
| assay: Hi-C |
| accession: ENCFF134PUN |
| validation_status: ok |
| api_url: https://www.encodeproject.org/files/ENCFF134PUN/ |
| status: archived |
| assembly: GRCh38 |
| file_format: bed |
| output_type: contact domains |
| file_size: 58070147883 |
| md5sum: cd12d922bb71692d98f924c04e72d038 |
| biological_replicates: [] |
| technical_replicates: [] |
| dataset: /annotations/ENCSR382HAW/ |
| download_url: https://www.encodeproject.org/files/ENCFF134PUN/@@download/ENCFF134PUN.bed.gz |
| s3_uri: s3://encode-public/2023/04/12/9c79af08-d830-4e4d-ae35-bae09c98b328/ENCFF134PUN.bed.gz |
| - family: rna_expression |
| provider: Roadmap Epigenomics |
| biosample: K562 mapping to verify |
| assay: RNA expression |
| identifier: 57epigenomes.RPKM.pc.gz |
| usage: target-gene expression and label-power covariates |
| validation_status: manual_required |
|
|
