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encode-chip-seq-subset

Tasks:
Feature Extraction
Size:
10M<n<100M
Tags:
biology
genomics
ChIP-seq
epigenomics
histone-modifications
ENCODE
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encode-chip-seq-subset / README.md
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Upload ENCODE Histone ChIP-seq subset (46 bigWig, ~38.7 GB)
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metadata 
license: cc0-1.0
task_categories:
  - feature-extraction
tags:
  - biology
  - genomics
  - ChIP-seq
  - epigenomics
  - histone-modifications
  - ENCODE
size_categories:
  - 10M<n<100M

ENCODE Histone ChIP-seq Subset (bigWig signal tracks)

Subset of Histone ChIP-seq signal tracks (bigWig format) downloaded from the ENCODE consortium. This is a convenience subset for vectorization / embedding experiments — it is not the full ENCODE release.

Contents

  • 46 bigWig files, ~38.7 GB total
  • 3 histone marks: H3K27ac, H3K4me3, H3K27me3
  • 7 experiments (ENCSR accessions):
    • ENCSR349EHZ (10 files)
    • ENCSR491RBV (10 files)
    • ENCSR527FRO (10 files)
    • ENCSR714ZJT (10 files)
    • ENCSR837DVF (2 files)
    • ENCSR864OOO (2 files)
    • ENCSR954JMZ (2 files)
  • Assemblies:
    • 40 files on mm10 (mouse, 56–57 chromosomes, ~2729 Mb genome)
    • 6 files on hg38 (human, 160–166 chromosomes incl. alt scaffolds, ~3100 Mb genome)
  • File size range: 0.51 GB – 1.28 GB per file

File naming 

<ENCSR_accession>_<ENCFF_accession>.bigWig

Example: ENCSR527FRO_ENCFF713EIC.bigWig

The ENCSR prefix identifies the experiment; the ENCFF prefix identifies the specific signal file (replicate / treatment / control). Look up metadata at https://www.encodeproject.org/experiments/<ENCSR_accession>/.

Signal distribution (sampled from ENCSR527FRO_ENCFF713EIC.bigWig, chr1, 500 bins × 100 kb)

Statistic Mean per bin Peak per bin
min 0.0002 0.0002
max 11.35 455.77
mean 0.54 40.14
median 0.13 9.59
stdev 1.05 —

Distribution is strongly right-skewed (median ≪ mean), as expected for ChIP-seq signal tracks: most of the genome is intergenic background with sparse, sharp peaks at binding/enrichment sites.

Provenance

  • Source: ENCODE Data Coordination Center
  • Downloaded: 2026-08-16 via download_encode_v2.py (filtered for assay_title=Histone+ChIP-seq, target.label in {H3K27ac, H3K4me3, H3K27me3}, status=released, .bigWig files only, capped at ~38 GB).
  • Original accessions: see filenames; each maps to a public ENCODE experiment.
  • No transformation: files are byte-identical to the ENCODE originals.

License

ENCODE data is released under a permissive license; see https://www.encodeproject.org/about/terms-of-use/. This subset is redistributed under CC0 for convenience. Attribution to ENCODE is requested for any derivative use.