type: position_score
table:
  filename: ENCFF065OBK.tabix.bed.gz
  header_mode: none
  zero_based: true
  format: tabix
  chrom:
    column_index: 0
  pos_begin:
    column_index: 1
  pos_end:
    column_index: 2
scores:
- id: TF_ChIP-seq_ENCSR706OJM
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR706OJM [biosample_summary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens POU6F1 treated with 6 \u03BCM\ \ all-trans-retinoic acid for 48 hours" and target="POU6F1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR706OJM [biosample_summary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens POU6F1 treated with 6 \u03BCM\ \ all-trans-retinoic acid for 48 hours" and target="POU6F1"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: treated with 6 \u03BCM all-trans-retinoic acid for 48 hours genetically\
    \ modified (insertion) using CRISPR targeting H. sapiens POU6F1\n\n**output\\\
    _type**: IDR thresholded peaks\n\n**audit\\_internal\\_action**: Released analysis\
    \ {ENCAN124ZQW|/analyses/ENCAN124ZQW/} has in progress subobject quality standard\
    \ {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\n**audit\\_warning**:\
    \ Processed alignments file {ENCFF597YLH|/files/ENCFF597YLH/} processed by ChIP-seq\
    \ ENCODE4 v1.8.0 GRCh38 pipeline has 19619054 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting POU6F1-human\
    \ and investigated as a transcription factor is 10 million usable fragments. The\
    \ recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE\
    \ ChIP-seq data standards|/data-standards/chip-seq/} )\n\n**audit\\_warning**:\
    \ Processed alignments file {ENCFF455UET|/files/ENCFF455UET/} processed by ChIP-seq\
    \ ENCODE4 v1.8.0 GRCh38 pipeline has 18371119 usable fragments. The minimum ENCODE\
    \ standard for each replicate in a ChIP-seq experiment targeting POU6F1-human\
    \ and investigated as a transcription factor is 10 million usable fragments. The\
    \ recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE\
    \ ChIP-seq data standards|/data-standards/chip-seq/} )\n\n**audit\\_warning**:\
    \ PBC1 (PCR Bottlenecking Coefficient 1, M1/M\\_distinct) is the ratio of the\
    \ number of genomic locations where exactly one read maps uniquely (M1) to the\
    \ number of genomic locations where some reads map (M\\_distinct). A PBC1 value\
    \ in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking,\
    \ 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value >\
    \ 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file\
    \ {ENCFF597YLH|/files/ENCFF597YLH/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.80.\n\n**audit\\\
    _warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the\
    \ number of genomic locations where exactly one read maps uniquely (M1) to the\
    \ number of genomic locations where two reads map uniquely (M2). A PBC2 value\
    \ in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking,\
    \ 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,\
    \ but > 3 is acceptable. ENCODE processed alignments file {ENCFF597YLH|/files/ENCFF597YLH/}\
    \ processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 4.79.\n\n**audit\\_warning**: NRF (Non Redundant Fraction)\
    \ is equal to the result of the division of the number of reads after duplicates\
    \ removal by the total number of reads. An NRF value in the range 0 - 0.5 is poor\
    \ complexity, 0.5 - 0.8 is moderate complexity, and > 0.8 high complexity. NRF\
    \ value > 0.8 is recommended, but > 0.5 is acceptable. ENCODE processed alignments\
    \ file {ENCFF455UET|/files/ENCFF455UET/} processed by ChIP-seq ENCODE4 v1.8.0\
    \ GRCh38 pipeline was generated from a library with NRF value of 0.78.\n\n**audit\\\
    _warning**: PBC1 (PCR Bottlenecking Coefficient 1, M1/M\\_distinct) is the ratio\
    \ of the number of genomic locations where exactly one read maps uniquely (M1)\
    \ to the number of genomic locations where some reads map (M\\_distinct). A PBC1\
    \ value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking,\
    \ 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value >\
    \ 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file\
    \ {ENCFF455UET|/files/ENCFF455UET/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.77.\n\n**audit\\\
    _warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the\
    \ number of genomic locations where exactly one read maps uniquely (M1) to the\
    \ number of genomic locations where two reads map uniquely (M2). A PBC2 value\
    \ in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking,\
    \ 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,\
    \ but > 3 is acceptable. ENCODE processed alignments file {ENCFF455UET|/files/ENCFF455UET/}\
    \ processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 4.28.\n\n**audit\\_warning**: Replicate concordance in ChIP-seq\
    \ experiments is measured by calculating IDR values (Irreproducible Discovery\
    \ Rate). ENCODE processed IDR thresholded peaks files {ENCFF065OBK|/files/ENCFF065OBK/}\
    \ processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline have a rescue ratio of\
    \ 2.98 and a self consistency ratio of 1.05. According to ENCODE standards, having\
    \ both rescue ratio and self consistency ratio values < 2 is recommended, but\
    \ having only one of the ratio values < 2 is acceptable."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR706OJM
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: "treated with 6 \u03BCM all-trans-retinoic acid for\
      \ 48 hours genetically modified (insertion) using CRISPR targeting H. sapiens\
      \ POU6F1"
    biosample_summary: "Homo sapiens SK-N-SH genetically modified (insertion) using\
      \ CRISPR targeting H. sapiens POU6F1 treated with 6 \u03BCM all-trans-retinoic\
      \ acid for 48 hours"
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0003072/
    perturbed: false
    doi: 10.17989/ENCSR706OJM
    date_created: '2020-09-08T22:13:21.835891+00:00'
    date_released: '2021-03-31'
    submitter_comment: ''
    target: POU6F1