Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
(A) Schematic of poly adenine-tailed gRNA (25A-gRNA) structure. Highlighted regions constitute the gRNA transcript, while unhighlighted regions flanking the gRNA transcript are part of the plasmid but not the transcript. The FE-modified gRNA hairpin is as in Chen et al.  (B) Flow cytometry plot comparing effectiveness of three wildtype gRNAs (wt-gRNAs) and 25A-gRNAs at knockout of GFP in Zfp42GFP mESCs after stable transfection along with Cas9. Horizontal segments indicate gates for GFP+ and GFP- cells (C) RT-qPCR comparison of wt-gRNA vs 25A-gRNA abundance using two different forms of dT priming, normalized to Actb expression.