type: position_score
table:
  filename: ENCFF243JXS.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_ENCSR213QOZ
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR213QOZ [TISSUE: Homo sapiens HepG2 genetically modified
    (insertion) using CRISPR targeting H. sapiens SMAD1, TARGET: SMAD1]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2


    **summary**: genetically modified (insertion) using CRISPR targeting H. sapiens
    SMAD1


    **output\_type**: IDR thresholded peaks


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has replaced subobject file {3616f164-259d-4a0c-b830-d90e3a47f53e|/files/3616f164-259d-4a0c-b830-d90e3a47f53e/}


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has replaced subobject file {54529bbd-4fac-4e0b-8983-e153b076c73e|/files/54529bbd-4fac-4e0b-8983-e153b076c73e/}


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has replaced subobject file {09e03f5d-d3eb-415e-b182-f269bb0ec6ba|/files/09e03f5d-d3eb-415e-b182-f269bb0ec6ba/}


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has in progress subobject document {0837f515-a130-40f8-be9d-0cc47dd8a146|/documents/0837f515-a130-40f8-be9d-0cc47dd8a146/}


    **audit\_internal\_action**: Released analysis {ENCAN348NIS|/analyses/ENCAN348NIS/}
    has replaced subobject file {b402214c-bf99-4ce8-a837-13f1adb9e7fd|/files/b402214c-bf99-4ce8-a837-13f1adb9e7fd/}


    **audit\_warning**: Processed alignments file {ENCFF968XFW|/files/ENCFF968XFW/}
    processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 19734125 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    SMAD1-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/} )


    **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 {ENCFF968XFW|/files/ENCFF968XFW/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38
    pipeline was generated from a library with PBC1 value of 0.89.


    **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 {ENCFF968XFW|/files/ENCFF968XFW/}
    processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library
    with PBC2 value of 8.90.


    **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 {ENCFF781SQE|/files/ENCFF781SQE/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38
    pipeline was generated from a library with PBC1 value of 0.90.


    **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 {ENCFF781SQE|/files/ENCFF781SQE/}
    processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library
    with PBC2 value of 9.72.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF243JXS|/files/ENCFF243JXS/} processed by ChIP-seq
    ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.94 and a self consistency
    ratio of 5.36. 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.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF892OZT|/files/ENCFF892OZT/} processed by ChIP-seq
    ENCODE4 v1.4.0 GRCh38 pipeline have a rescue ratio of 1.94 and a self consistency
    ratio of 5.36. 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: ENCSR213QOZ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using CRISPR targeting
      H. sapiens SMAD1
    biosample_summary: Homo sapiens HepG2 genetically modified (insertion) using CRISPR
      targeting H. sapiens SMAD1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR213QOZ
    date_created: '2019-12-20T05:37:19.118551+00:00'
    date_released: '2020-08-17'
    submitter_comment: ''
    target: SMAD1
