The paper introduces and explains Perturb-seq, a new experimental and computational technology that combines pooled CRISPR-based genetic screening with single-cell RNA sequencing (scRNA-seq) to analyze complex biological circuits. This method allows researchers to study the transcriptional effects and genetic interactions of numerous perturbations simultaneously within individual cells. The accompanying computational framework, MIMOSCA, is designed to estimate the impact of these perturbations on gene expression, cellular states, and gene programs, proving robust even when accounting for biological and technical covariates like cell quality or cell cycle phase. Through applications in immune cells (BMDCs) and K562 cell lines, the researchers demonstrate Perturb-seq's ability to accurately identify regulatory modules and opposing cellular programs, showing that fewer cells and reads are needed to detect effects on gene signatures compared to individual genes.

References:

• Dixit A, Parnas O, Li B, et al. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens[J]. cell, 2016, 167(7): 1853-1866. e17.