Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted anti-cancer therapy

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted anti-cancer therapy Overall design: Single-cell RNA-seq libraries were generated using three-level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of untreated or small molecule inhibitor exposed A172, T98G, U87MG, GBM4, GBM8, GSC0131, and GSC0827 glioblastoma brain cancer cells. In a subset of experiments A172, T98G and U87MG engineered to express dCas9-KRAB or dCas9-SunTag for CRISPR/Cas9 mediated gene knockdown or overexpression, respectively, were genetically perturbed for HPRT1, components of the mismatch repair machinery, 522 protein kinases. Different cells and different treatments were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on the fixation of barcodes containing well-specific oligos that are specific to a given cell type, replicate, or treatment condition. For genetically perturbed experiments, targeted capture and enrichment of gRNA-containing transcripts were performed.