Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]

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. MultiPerturb-seq data consists of single-cell ATAC-seq, RNA-seq, and CRISPR guide RNA capture for BT16 cells transduced with a CRISPR library to knock-down epigenomic remodelers and a 20% spike-in of NIH3T3 cells transduced with non-targeting guide RNAs. In addition, CUT&RUN data (H2A.Z and H3K4me3) is from BT16 cells that received either non-targeting (NT) or ZNHIT1-targeting guide RNAs.