Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
(A) UCSC browser track showing MERA screen ratio of gRNA abundance in Msh2GFP- vs bulk pools for ~12,000 gRNAs tiled across the Msh2 cis-regulatory region in mESCs. ENCODE histone modification tracks are shown underneath plot, and gRNAs chosen for follow-up are highlighted. (B) Flow cytometry plot showing Msh2GFP/mCherry mESC line before CRISPR/Cas9 targeting. (C) Flow cytometry plots of Msh2GFP/mCherry mESCs after targeting with three cis-gRNAs, showing infrequent biallelic loss of expression.