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Genentech
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GM12878_dnase-data

Name: GM12878_dnase-data
Creator: Genentech
License: https://choosealicense.com/licenses/mit/

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GM12878_dnase-data

Dataset Summary

This dataset contains genomic intervals used to train a regression model on GM12878 DNase data, described in Lal et al. 2025 (https://www.nature.com/articles/s41592-025-02868-z). Genome coordinates correspond to the hg38 reference genome.

Repository Content

The repository includes one BED file and one Jupyter notebook:

intervals.bed: Genomic intervals stored in BED format.
1_process_GM12878_data.ipynb: Jupyter notebook containing the preprocessing steps used to generate the intervals.bed file.

Dataset Structure

1. Intervals file (`intervals.bed`)

BED format (tab-separated). There are three columns with no header. All intervals have length 2114 bp.

Chromosome name.
start position.
end position.

Usage

from huggingface_hub import hf_hub_download
import pandas as pd

file_path = hf_hub_download(repo_id="Genentech/GM12878_dnase-data", filename="intervals.bed")
df_human = pd.read_csv(file_path, sep='\t', header=None)