type: position_score
table:
  filename: ENCFF432QDG.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: Histone_ChIP-seq_ENCSR662PLB
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR662PLB [TISSUE: Homo sapiens neuroepithelial stem cell stably
    expressing HES5 originated from H9, TARGET: H3K4me3]'
  description: '**status**: released


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


    **summary**: female embryo (5 days) stably expressing C-terminal eGFP-tagged HES5


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN619XAA|/analyses/ENCAN619XAA/}
    has in progress subobject document {f75e76ac-0c7a-4994-b33e-1682877cd323|/documents/f75e76ac-0c7a-4994-b33e-1682877cd323/}


    **audit\_internal\_action**: Released analysis {ENCAN619XAA|/analyses/ENCAN619XAA/}
    has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/}


    **audit\_warning**: Processed alignments file {ENCFF512LUQ|/files/ENCFF512LUQ/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 16965006 usable fragments.
    The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me3-human and investigated as a narrow histone mark 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 {ENCFF753GNS|/files/ENCFF753GNS/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.85.


    **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 {ENCFF753GNS|/files/ENCFF753GNS/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 7.39.


    **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 {ENCFF512LUQ|/files/ENCFF512LUQ/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.73.


    **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 {ENCFF512LUQ|/files/ENCFF512LUQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.72.


    **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 {ENCFF512LUQ|/files/ENCFF512LUQ/}
    processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 3.37.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR662PLB
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female embryo (5 days) stably expressing C-terminal
      eGFP-tagged HES5
    biosample_summary: Homo sapiens neuroepithelial stem cell stably expressing HES5
      originated from H9
    replication_type: isogenic
    biosample_ontology: /biosample-types/in_vitro_differentiated_cells_CL_0002259/
    perturbed: false
    doi: 10.17989/ENCSR662PLB
    date_created: '2015-02-20T02:37:01.021863+00:00'
    date_released: '2016-05-20'
    submitter_comment: As of March 30th, 2017, this experiment has been rerun on both
      GRCh38 and hg19 using replicates 1 and 3.
    target: H3K4me3