type: position_score
table:
  filename: ENCFF594LVO.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_ENCSR000ALC
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR000ALC [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K36me3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR000ALC [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="H3K36me3"]'
  description: '**status**: released


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


    **summary**: newborn


    **output\_type**: replicated peaks


    **audit\_error**: Processed alignments file {ENCFF571XAD|/files/ENCFF571XAD/}
    processed by ChIP-seq ENCODE3 hg19 pipeline has 999999 usable fragments. The minimum
    ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human
    and investigated as a broad histone mark is 20 million usable fragments. The recommended
    value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data
    standards|/data-standards/chip-seq/})


    **audit\_internal\_action**: Archived analysis {ENCAN586WEO|/analyses/ENCAN586WEO/}
    has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF449FVX|/files/ENCFF449FVX/}
    processed by ChIP-seq ENCODE3 hg19 pipeline has 5403144 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments.
    The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE
    ChIP-seq data standards|/data-standards/chip-seq/})


    **audit\_not\_compliant**: Processed alignments file {ENCFF140AOS|/files/ENCFF140AOS/}
    processed by ChIP-seq ENCODE3 hg19 pipeline has 7896082 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments.
    The recommended value is > 45 million, but > 35 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 {ENCFF571XAD|/files/ENCFF571XAD/} processed by ChIP-seq ENCODE3 hg19 pipeline
    was generated from a library with PBC1 value of 0.83.


    **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 {ENCFF571XAD|/files/ENCFF571XAD/}
    processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with
    PBC2 value of 6.13.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000ALC
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: newborn
    biosample_summary: Homo sapiens endothelial cell of umbilical vein newborn
    replication_type: anisogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002618/
    perturbed: false
    doi: 10.17989/ENCSR000ALC
    date_created: '2013-11-07T22:16:13.633394+00:00'
    date_released: '2011-02-10'
    submitter_comment: As of August 2022, the donors associated with the biosamples
      in this dataset were changed from ENCDO551FXN to ENCDO466MPW and ENCDO560UMK.
      See PMID:32728101.
    target: H3K36me3