type: position_score
table:
  filename: ENCFF833UNB.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_ENCSR000EKF
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'DNase-seq ENCSR000EKF [TISSUE: Homo sapiens endothelial cell of umbilical
    vein newborn]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: newborn


    **output\_type**: peaks


    **audit\_internal\_action**: Released analysis {ENCAN390QWY|/analyses/ENCAN390QWY/}
    has in progress subobject document {2f35d34b-ff7c-4790-b888-2a2f90a0ed0f|/documents/2f35d34b-ff7c-4790-b888-2a2f90a0ed0f/}


    **audit\_warning**: Alignment file {ENCFF091KTX|/files/ENCFF091KTX/} processed
    by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/}
    ) for GRCh38 assembly has 28233440 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 {ENCFF091KTX|/files/ENCFF091KTX/} processed by DNase-seq ENCODE4
    v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly  have
    a SPOT1 score of 0.37. 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: ENCSR000EKF
    status: released
    assay_term_name: DNase-seq
    simple_biosample_summary: newborn
    biosample_summary: Homo sapiens endothelial cell of umbilical vein newborn
    replication_type: unreplicated
    biosample_ontology: /biosample-types/primary_cell_CL_0002618/
    perturbed: false
    doi: 10.17989/ENCSR000EKF
    date_created: '2014-01-30T18:55:30.519438+00:00'
    date_released: '2011-04-19'
    submitter_comment: As of August 2022, the donors associated with the biosamples
      in this dataset were changed from ENCDO000AAS to ENCDO466MPW and ENCDO560UMK.
      See PMID:32728101.
