Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1. Single nucleus ATAC-seq, RNA-seq, and CRISPR guide RNA capture for BT16 cells transduced with an epigenomic remodeler library and a 20% spike-in of NIH3T3 cells transduced with non-targeting guides.