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Datasets:
fabricioslv
/
encode-chip-seq-subset

Tasks:
Feature Extraction
Size:
10M<n<100M
Tags:
biology
genomics
ChIP-seq
epigenomics
histone-modifications
ENCODE
License:
Dataset card Files
xet
 Community
fabricioslv commited on
Commit
7e71c23
·
verified ·
1 Parent(s): 38e1e46

Upload ENCODE Histone ChIP-seq subset (46 bigWig, ~38.7 GB)

Browse files
Files changed (48) hide show
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+ ---
2
+ license: cc0-1.0
3
+ task_categories:
4
+ - feature-extraction
5
+ tags:
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+ - biology
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+ - genomics
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+ - ChIP-seq
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+ - epigenomics
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+ - histone-modifications
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+ - ENCODE
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+ size_categories:
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+ - 10M<n<100M
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+ ---
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+
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+ # ENCODE Histone ChIP-seq Subset (bigWig signal tracks)
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+
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+ Subset of **Histone ChIP-seq** signal tracks (bigWig format) downloaded from the
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+ [ENCODE](https://www.encodeproject.org/) consortium. This is a convenience subset
20
+ for vectorization / embedding experiments — it is **not** the full ENCODE release.
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+
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+ ## Contents
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+
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+ - **46 bigWig files**, ~38.7 GB total
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+ - **3 histone marks**: H3K27ac, H3K4me3, H3K27me3
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+ - **7 experiments** (ENCSR accessions):
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+ - `ENCSR349EHZ` (10 files)
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+ - `ENCSR491RBV` (10 files)
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+ - `ENCSR527FRO` (10 files)
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+ - `ENCSR714ZJT` (10 files)
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+ - `ENCSR837DVF` (2 files)
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+ - `ENCSR864OOO` (2 files)
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+ - `ENCSR954JMZ` (2 files)
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+ - **Assemblies**:
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+ - 40 files on **mm10** (mouse, 56–57 chromosomes, ~2729 Mb genome)
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+ - 6 files on **hg38** (human, 160–166 chromosomes incl. alt scaffolds, ~3100 Mb genome)
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+ - **File size range**: 0.51 GB – 1.28 GB per file
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+
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+ ## File naming
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+
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+ ```
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+ <ENCSR_accession>_<ENCFF_accession>.bigWig
43
+ ```
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+
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+ Example: `ENCSR527FRO_ENCFF713EIC.bigWig`
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+
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+ The `ENCSR` prefix identifies the experiment; the `ENCFF` prefix identifies the
48
+ specific signal file (replicate / treatment / control). Look up metadata at
49
+ `https://www.encodeproject.org/experiments/<ENCSR_accession>/`.
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+
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+ ## Signal distribution (sampled from `ENCSR527FRO_ENCFF713EIC.bigWig`, chr1, 500 bins × 100 kb)
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+
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+ | Statistic | Mean per bin | Peak per bin |
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+ |---|---|---|
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+ | min | 0.0002 | 0.0002 |
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+ | max | 11.35 | 455.77 |
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+ | mean | 0.54 | 40.14 |
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+ | median | 0.13 | 9.59 |
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+ | stdev | 1.05 | — |
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+
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+ Distribution is strongly right-skewed (median ≪ mean), as expected for ChIP-seq
62
+ signal tracks: most of the genome is intergenic background with sparse, sharp
63
+ peaks at binding/enrichment sites.
64
+
65
+ ## Provenance
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+
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+ - **Source**: ENCODE Data Coordination Center
68
+ - **Downloaded**: 2026-08-16 via `download_encode_v2.py` (filtered for
69
+ `assay_title=Histone+ChIP-seq`, `target.label` in {H3K27ac, H3K4me3, H3K27me3},
70
+ `status=released`, `.bigWig` files only, capped at ~38 GB).
71
+ - **Original accessions**: see filenames; each maps to a public ENCODE experiment.
72
+ - **No transformation**: files are byte-identical to the ENCODE originals.
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+
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+ ## License
75
+
76
+ ENCODE data is released under a permissive license; see
77
+ https://www.encodeproject.org/about/terms-of-use/. This subset is redistributed
78
+ under CC0 for convenience. Attribution to ENCODE is requested for any derivative use.