| --- |
| 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](https://www.encodeproject.org/) 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. |
|
|
