---
license: cc-by-4.0
pretty_name: KOLF2.1J Perturbation Cell Atlas (h5ad)
tags:
  - biology
  - single-cell
  - perturb-seq
  - crispri
  - genomics
  - ipsc
  - anndata
task_categories:
  - feature-extraction
---

# KOLF2.1J Perturbation Cell Atlas — raw `.h5ad`

This repository is a **mirror** of the raw AnnData (`.h5ad`) files from the
**KOLF2.1J Perturbation Cell Atlas**, a genome-scale CRISPRi Perturb-seq atlas of
human induced pluripotent stem cells (iPSCs).

> **This is not original work by the uploader.** The data were produced by Doctor,
> Nourreddine, and Mali, released under **CC BY 4.0**, and are re-hosted here only
> to make the raw `.h5ad` files easier to download. All credit belongs to the
> original authors; please cite them (see **Citation** below).

## Provenance

| | |
|---|---|
| **Original title** | *A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells* |
| **Authors** | Yesh Doctor, Sami Nourreddine, Prashant Mali |
| **Source dataset** | figshare, DOI [`10.25452/figshare.plus.27261219.v1`](https://doi.org/10.25452/figshare.plus.27261219.v1) |
| **License** | Creative Commons Attribution 4.0 International (CC BY 4.0) |
| **Associated preprint** | [`10.1101/2024.11.03.621734`](https://doi.org/10.1101/2024.11.03.621734) |
| **Analysis code** | https://github.com/y-doctor/KOLF2.1J_Perturbation_Cell_Atlas (MIT) |

## Files

All files are [AnnData](https://anndata.readthedocs.io/) `.h5ad` (HDF5). Sizes and
MD5 checksums are listed below; verify after download with `md5sum`.

| File | Size | MD5 |
|---|---:|---|
| `KOLF_Metabolic_Enzymes_Strong_Perturbations.h5ad` | 1.23 GB | `95f57fd679b98ba4f060d143959c3a66` |
| `KOLF_Chromatin_Modifiers_Strong_Perturbations.h5ad` | 1.42 GB | `fbd62eee013ad01be10f8ff291c8f8f5` |
| `KOLF_Chromatin_Modifiers_QC_Filtered.h5ad` | 4.32 GB | `246eda29efaf8ae8da86c39840678582` |
| `KOLF_Metabolic_Enzymes_QC_Filtered.h5ad` | 6.50 GB | `b5e17ab928cf263f679cf63bbb311a25` |
| `KOLF_Strong_Perturbations.h5ad` | 43.51 GB | `28bcfff0679e7c6c35bdd584f3626362` |
| `KOLF_Pan_Genome_QC_Filtered.h5ad` | 176.4 GB | `afd30fde1e6ad32969c29868394385d1` |

`checksums.md5` in this repo contains the same checksums in `md5sum -c` format.

> **Note on the large file.** `KOLF_Pan_Genome_QC_Filtered.h5ad` is ~176 GiB. Use
> streaming/backed reads (`anndata.read_h5ad(path, backed="r")`) unless you have
> enough RAM to load it in full.

## Usage

```python
from huggingface_hub import hf_hub_download
import anndata as ad

path = hf_hub_download(
    repo_id="Boom5426/KOLF",
    repo_type="dataset",
    filename="KOLF_Chromatin_Modifiers_Strong_Perturbations.h5ad",
)
adata = ad.read_h5ad(path, backed="r")
print(adata)
```

## Citation

If you use these data, cite the original authors:

```bibtex
@article{doctor2024kolf,
  title   = {A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells},
  author  = {Doctor, Yesh and Nourreddine, Sami and Mali, Prashant},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.11.03.621734}
}
```

Dataset: Doctor Y., Nourreddine S., Mali P. *KOLF2.1J Perturbation Cell Atlas.*
figshare. DOI [`10.25452/figshare.plus.27261219.v1`](https://doi.org/10.25452/figshare.plus.27261219.v1). CC BY 4.0.