Yfeng0216/Perturb_DBiT

Perturb-DBiT

Mirror of the original sequencing files and GEO supplementary archives associated with Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT.

Paper: https://doi.org/10.1038/s41587-026-03127-y

Contents

• raw/: 36 original compressed FASTQ files, comprising paired reads for 18 sequencing runs.
• processed/: the original GSE319277_RAW.tar and GSE319123_RAW.tar supplementary archives from GEO, preserved as distributed.
• metadata/files.json: original download URLs, exact file sizes, and checksum information.
• metadata/ena_runs.tsv: ENA run metadata and official FASTQ checksums.
• checksums/md5.txt: the official ENA MD5 values for all 36 FASTQ files.
• checksums/sha256.txt: locally computed SHA-256 values for the two downloaded GEO archives.

The 38 data files total 308,629,897,773 bytes (308.63 GB). Data archives are stored without recompression or filtering.

Original sources

• GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE319277
• GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE319123
• BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1422738
• ENA: https://www.ebi.ac.uk/ena/browser/view/PRJNA1422738

Integrity

All 36 FASTQ files were checked against the official ENA MD5 values. The two GEO archives were checked against the published archive member lists and sizes; their local SHA-256 values are included for subsequent download verification.

On Linux, run md5sum -c checksums/md5.txt and sha256sum -c checksums/sha256.txt from the downloaded repository directory.

Download

These are sequencing files and supplementary archives, rather than a tabular dataset. Download them with the Hugging Face Hub:

from huggingface_hub import snapshot_download

snapshot_download(
    repo_id="Yfeng0216/Perturb_DBiT",
    repo_type="dataset",
    local_dir="Perturb_DBiT",
)

Please cite the original study and retain the original data accession references when using this mirror.

Alignment reference files

The separate references/ folder contains the complete GENCODE mouse GRCm39 (M29) and human GRCh38.p13 (v39) FASTA files, with the corresponding GTF annotations.

These four additional compressed files total 1.74 GB, separate from the 308.63 GB of original experimental data above. Official GENCODE MD5 values, SHA-256 checksums, source URLs, and verification details are included in that folder.