CRISPRi Perturbation Atlas of Human Stem Cells with 11,739 Genes

A genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J human induced pluripotent stem cells (hiPSCs) maps transcriptional phenotypes associated with 11,739 perturbed genes across more than 2.5 million single cells. The dataset was generated by Yesh Doctor and published on figshare in May 2026. It includes expressed genome-wide and pilot screen datasets for chromatin modifiers and metabolic enzymes.

Use Cases

• Mapping genotype-phenotype relationships based on transcriptional phenotypes from perturbed genes.
• Identifying novel regulators of pluripotency based on correlations between perturbed phenotypes.
• Discovering RNA editing modulators based on genome-scale screening via transcriptome-wide RNA editing.
• Analyzing functionally related protein complexes based on recapitulation patterns in the cell map.

Strengths

• Covers 11,739 perturbed genes.
• Includes data from more than 2.5 million single cells.
• Dataset size is 233.4 GB, indicating substantial depth.
• Includes subsets focused on strong perturbations and specific gene classes (chromatin modifiers, metabolic enzymes).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data is specific to KOLF2.1J human induced pluripotent stem cells, limiting generalizability.

Provenance

Source

figshare

Collection Method

Generated via expressed genome-scale CRISPRi Perturb-Seq.

Freshness

Last updated 2026-05-18 23:49:45; freshness should be verified.