genome wide pertub-seq

 CRISPi + scRNA

https://gwps.wi.mit.edu/

matrix file in H5AD format

https://doi.org/10.25452/figshare.plus.20029387

Genome wide screen targeted n=9867 genes. 

Essential-wide screen targeted n=2285 essential genes. 

Growth phenotypes were measured log2-guide enrichment per cell doubling (gamma)

"The relative homogeneity of CRISPRi reduces selection for unperturbed cells, especially when studying essential genes.  Unlike CRISPR knockout, CRISPRi does not lead to activation of the DNA damage response which can alter transcriptional signatures (Haapaniemi et al., 2018)."

"We use a compact, multiplexed CRISPR interference (CRISPRi) library to assay thousands of loss-of-function genetic perturbations with single-cell RNA sequencing (scRNA-seq) in chronic myeloid leukemia (CML) (K562) and retinal pigment epithelial (RPE1) cell lines."

There are four datasets on SRA:

1. K562 day 8 Perturb-seq (KD8): targeting all expressed genes at day 8 after transduction
2. RPE1 day 7 Perturb-seq (RD7): targeting DepMap essential genes at day 7 after transduction
3. K562 day 6 Perturb-seq (KD7): targeting DepMap essential genes at day 6 after transduction
4. K562 day 8 Perturb-seq (KD8_ultima): scRNA-seq libraries from the KD8 experiment sequenced on the Ultima sequencing platform rather than the Illumina sequencing platform

Potential problem: essential gene cannot be deleted? 

This is good data set for graph controllability, graph neural network analysis.