type: position_score
table:
  filename: ENCFF638SXR.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_ENCSR000BPL
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR000BPL [TISSUE: Homo sapiens SK-N-MC, TARGET: POLR2AphosphoS5]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: IDR thresholded peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN670HFU|/analyses/ENCAN670HFU/} has in progress\
    \ subobject document {a37a6b7b-9f46-4907-adf2-e9d42e99510c|/documents/a37a6b7b-9f46-4907-adf2-e9d42e99510c/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN670HFU|/analyses/ENCAN670HFU/}\
    \ has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/}\n\
    \n**audit\\_warning**: Processed alignments file {ENCFF830JTI|/files/ENCFF830JTI/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14240675 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ POLR2AphosphoS5-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**: 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 {ENCFF854PCK|/files/ENCFF854PCK/} processed by ChIP-seq ENCODE4 v1.6.1\
    \ GRCh38 pipeline was generated from a library with PBC1 value of 0.85.\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 {ENCFF854PCK|/files/ENCFF854PCK/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library\
    \ with PBC2 value of 6.54.\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 {ENCFF638SXR|/files/ENCFF638SXR/}\
    \ processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of\
    \ 2.15 and a self consistency ratio of 1.05. 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: ENCSR000BPL
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens SK-N-MC
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0002860/
    perturbed: false
    doi: 10.17989/ENCSR000BPL
    date_created: '2013-09-13T15:57:57.510048-08:00'
    date_released: '2012-02-29'
    submitter_comment: ChIP-seq against POLR2AphosphoS5 using SK-N-MC cell line which
      was previously described as a neuroepithelioma (ATCC HTB-10). However recent
      evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687,
      www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
    target: POLR2AphosphoS5