TruthSeq: Processed Perturb-seq Knockdown Z-scores for K562 Cells

Approximately 11,000 individual gene knockdowns in K562 cells are represented by z-scores for gene expression changes. This processed data from the Replogle Perturb-seq atlas is used to validate computational predictions of gene regulatory networks. The original raw data is available under GEO accession GSE132080.

Use Cases

• Validating computational gene regulatory predictions against experimental knockdown evidence.
• Analyzing the downstream expression effects of specific gene perturbations.
• Benchmarking network inference algorithms using a large-scale, standardized experimental dataset.

Strengths

• Contains data from a large-scale Perturb-seq experiment targeting ~11,000 genes.
• Provides processed, analysis-ready z-scores derived from a peer-reviewed atlas (Replogle et al., Cell 2022).
• Has a clear, open license (CC-BY-4.0) and links to the original raw data source.

Limitations

• Column names and exact row counts are not provided in the available metadata.
• Data is specific to a single cell line (K562), limiting generalizability.
• The dataset is processed; users needing raw counts must access the separate GEO archive.

Provenance

Source

Replogle Perturb-seq atlas (GEO accession GSE132080).

Collection Method

Experimental gene knockdowns followed by single-cell RNA sequencing (Perturb-seq).

Time Range

null

Freshness

Last updated 2026-03 24.

Geography

null