Datasets:

slaf-project
/

X-Atlas-Orion

viewer: true
license: cc-by-nc-sa-4.0
configs:
  - config_name: HEK293T-cells
    data_dir: data/HEK293T/cells.lance
  - config_name: HEK293T-expression
    data_dir: data/HEK293T/expression.lance
  - config_name: HEK293T-genes
    data_dir: data/HEK293T/genes.lance
  - config_name: HCT116-cells
    data_dir: data/HCT116/cells.lance
  - config_name: HCT116-expression
    data_dir: data/HCT116/expression.lance
  - config_name: HCT116-genes
    data_dir: data/HCT116/genes.lance
language:
  - en
tags:
  - biology
  - genomics
  - RNA
  - single-cell
  - lance
  - slaf
pretty_name: X-Atlas-Orion

X-Atlas Orion Dataset (SLAF Format)

Attribution

This is a re-release of data originally generated by Xaira Therapeutics.

Original Dataset: Xaira-Therapeutics/X-Atlas-Orion
Original Format: Parquet files
This Release: Same data in SLAF (Sparse Lazy Array Format)
License: CC-BY-NC-SA-4.0 (Creative Commons Attribution-NonCommercial-ShareAlike 4.0)
Original Citation:

@article{huang2025xatlasorion,
  title={X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models},
  author={Huang, Ann C and Hsieh, Tsung-Han S and Zhu, Jiang and Michuda, Jackson and Teng, Ashton and Kim, Soohong and Rumsey, Elizabeth M and Lam, Sharon K and Anigbogu, Ikenna and Wright, Philip and Ameen, Mohamed and You, Kwontae and Graves, Christopher J and Kim, Hyunsung John and Litterman, Adam J and Sit, Rene V  and Blocker, Alex and Chu, Ci},
  journal={bioRxiv},
  year={2025},
  url={https://www.biorxiv.org/content/10.1101/2025.06.11.659105v1}
}

For detailed information about the dataset, methodology, and original publication, please refer to the original dataset repository.

Dataset Description

X-Atlas/Orion is a Perturb-seq atlas containing two genome-wide Fix-Cryopreserve-ScRNAseq (FiCS) Perturb-seq screens that target all human protein-coding genes (n = 18,903 genes). The dataset is comprised of eight million HCT116 and HEK293T cells, each deeply sequenced to a median of 16,000 unique molecular identifiers (UMIs) per cell. The median on-target knockdown efficiency is 75.4% in HCT116 cells and 51.5% in HEK293T cells, with a median of at least 140 cells per perturbation. This release provides the same data in SLAF format for compatibility with SLAF tools. For more detailed information, see the original dataset repository.

Usage

This dataset is in SLAF (Sparse Lazy Array Format) format, which uses the Lance table format for storage. You can use it with the slafdb library (for SLAF format), or pylance library (for direct Lance access).

Using SLAF (Recommended for SLAF Format)

pip install slafdb

hf_path = 'hf://datasets/slaf-project/X-Atlas-Orion'
from slaf import SLAFArray
slaf_hct116 = SLAFArray(f"{hf_path}/data/HCT116")
slaf_hct116.query("SELECT * FROM cells LIMIT 10")

Using Lance Directly

pip install pylance

hf_path = 'hf://datasets/slaf-project/X-Atlas-Orion'
import lance
lance_hct116_ds = lance.dataset(f"{hf_path}/data/HCT116/cells.lance")
lance_hct116_ds.sample(10)