type: position_score
table:
  filename: ENCFF171XML.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_ENCSR949COJ
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR949COJ [biosample_summary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens ARNTL treated with 6 \u03BCM all-trans-retinoic\ \ acid for 48 hours" and target="ARNTL"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR949COJ [biosample_summary="Homo sapiens SK-N-SH genetically modified\ \ (insertion) using CRISPR targeting H. sapiens ARNTL treated with 6 \u03BCM all-trans-retinoic\ \ acid for 48 hours" and target="ARNTL"]'
  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 ARNTL\n\n**output\\_type**:\
    \ IDR thresholded peaks\n\n**audit\\_internal\\_action**: Released analysis {ENCAN303XRF|/analyses/ENCAN303XRF/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN303XRF|/analyses/ENCAN303XRF/}\
    \ has in progress subobject document {0a3cc4c1-bd3c-4a44-923d-f5be6765ea94|/documents/0a3cc4c1-bd3c-4a44-923d-f5be6765ea94/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF582KRM|/files/ENCFF582KRM/}\
    \ processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline has 17804273 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ ARNTL-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**: 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 {ENCFF582KRM|/files/ENCFF582KRM/}\
    \ processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.52.\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 {ENCFF582KRM|/files/ENCFF582KRM/} processed\
    \ by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.50.\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 {ENCFF582KRM|/files/ENCFF582KRM/} processed by ChIP-seq ENCODE4 v1.5.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 1.94.\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 {ENCFF897PPT|/files/ENCFF897PPT/}\
    \ processed by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.56.\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 {ENCFF897PPT|/files/ENCFF897PPT/} processed\
    \ by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline was generated from a library with\
    \ PBC1 value of 0.55.\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 {ENCFF897PPT|/files/ENCFF897PPT/} processed by ChIP-seq ENCODE4 v1.5.0\
    \ GRCh38 pipeline was generated from a library with PBC2 value of 2.14.\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 {ENCFF171XML|/files/ENCFF171XML/} processed by ChIP-seq ENCODE4\
    \ v1.5.0 GRCh38 pipeline have a rescue ratio of 1.48 and a self consistency ratio\
    \ of 2.06. 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.\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 {ENCFF836WHR|/files/ENCFF836WHR/} processed\
    \ by ChIP-seq ENCODE4 v1.5.0 GRCh38 pipeline have a rescue ratio of 1.48 and a\
    \ self consistency ratio of 2.06. 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: ENCSR949COJ
    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\
      \ ARNTL"
    biosample_summary: "Homo sapiens SK-N-SH genetically modified (insertion) using\
      \ CRISPR targeting H. sapiens ARNTL 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/ENCSR949COJ
    date_created: '2018-01-11T23:37:22.573559+00:00'
    date_released: '2020-07-07'
    submitter_comment: ''
    target: ARNTL