Abstract:

By combining droplet based single cell transcriptomics with CRISPR-Cas based perturbations we demonstrate the ability to perform thousands of genetic manipulations in a single pooled experiment. This represents a [100x...put [10x...put  actual number here] improvement in cost over current approaches. By increasing the number of cells per droplet we demonstrate that for a small reduction in sensitivity for differentially expressed genes that decrease in expression we gain a ten fold increase in sample size.  Finally, by randomly lentivirally integrating several sgRNAs in each cell, we show the ability to extend the method to perform combinatorially screens. The random structure of the experimental design matrix, so constructed, satisfies the incoherence properties in a compressed sensing framework. Together, these statistical and experimental methods will enable researchers to perform large scale screening of perturbations, including systematic dissection of epistatic effects, using RNA transcription as a phenotype.