Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens

Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations Overall design: scRNA-seq with pooled CRISPR-KO perturbations in 200,000 cells across six screens unstimulated BMDC, BMDC stimulated at 3hr, TFs in K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbations, *Note: that the raw SRA data consists of BAM files not FASTQ files