data/external/k562_molecular_sources_audit.yaml

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