type: position_score
table:
  filename: ENCFF992ZCX.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: DNase-seq_ENCSR618HFT
  column_index: 3
  type: float
  desc: 'DNase-seq ENCSR618HFT [biosample_summary="Homo sapiens stimulated activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR618HFT [biosample_summary="Homo sapiens stimulated activated CD4-positive, alpha-beta T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (42 years) treated with anti-CD3 and anti-CD28 coated
    beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour


    **output\_type**: peaks


    **audit\_warning**: Alignment file {ENCFF159XDU|/files/ENCFF159XDU/} processed
    by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/}
    ) for GRCh38 assembly has 21661012 mapped reads. According to ENCODE standards,
    conventional DNase-seq profile requires a minimum of 20 million uniquely mapped
    reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended
    value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million
    uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/})


    **audit\_warning**: Signal Portion of Tags (SPOT) is a measure of enrichment,
    analogous to the commonly used fraction of reads in peaks metric. ENCODE processed
    alignment files {ENCFF159XDU|/files/ENCFF159XDU/} processed by DNase-seq ENCODE4
    v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38
    assembly  have a SPOT1 score of 0.39. According to ENCODE standards, SPOT1 score
    of 0.4 or higher is considered a product of high quality data. Any sample with
    a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample,
    and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25
    is considered minimally acceptable for rare and hard to find primary tissues.
    (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/})'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR618HFT
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: male adult (42 years) treated with anti-CD3 and anti-CD28
      coated beads for 1 hour, 100 ng/mL TNF-alpha for 1 hour
    biosample_summary: Homo sapiens stimulated activated CD4-positive, alpha-beta
      T cell male adult (42 years) treated with anti-CD3 and anti-CD28 coated beads
      for 1 hour, 100 ng/mL TNF-alpha for 1 hour
    replication_type: unreplicated
    biosample_ontology: /biosample-types/primary_cell_NTR_0000663/
    perturbed: false
    doi: 10.17989/ENCSR618HFT
    date_created: '2020-04-20T23:46:03.311583+00:00'
    date_released: '2020-09-28'
    submitter_comment: ''
