type: position_score
table:
  filename: ENCFF565NIW.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_ENCSR146NLL
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR146NLL [TISSUE: Homo sapiens HEK293 genetically modified
    (insertion) using site-specific recombination targeting H. sapiens REPIN1, TARGET:
    REPIN1]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 3


    **summary**: genetically modified (insertion) using site-specific recombination
    targeting H. sapiens REPIN1


    **output\_type**: optimal IDR thresholded peaks


    **audit\_internal\_action**: File {ENCFF565NIW|/files/ENCFF565NIW/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_internal\_action**: Archived analysis {ENCAN299KVB|/analyses/ENCAN299KVB/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_warning**: Processed alignments file {ENCFF071SPF|/files/ENCFF071SPF/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13347471 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    REPIN1-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**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF277SUI|/files/ENCFF277SUI/}, {ENCFF565NIW|/files/ENCFF565NIW/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.44 and
    a self consistency ratio of 1.01. 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 {ENCFF607YXV|/files/ENCFF607YXV/}, {ENCFF881ZPZ|/files/ENCFF881ZPZ/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 2.44 and
    a self consistency ratio of 1.01. 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: ENCSR146NLL
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using site-specific
      recombination targeting H. sapiens REPIN1
    biosample_summary: Homo sapiens HEK293 genetically modified (insertion) using
      site-specific recombination targeting H. sapiens REPIN1
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001182/
    perturbed: false
    doi: 10.17989/ENCSR146NLL
    date_created: '2016-03-29T17:49:18.932044+00:00'
    date_released: '2017-03-07'
    submitter_comment: The archived libraries sequenced on HiSeq 2000 did not meet
      ENCODE read depth requirements. We have therefore provided more deeply sequenced
      data.
    target: REPIN1
