Next Generation Sequencing Analysis of the single-cell Transcriptomes of the K562-Cas9 cell infected with lentiviral sgRNA library containing programmed scaffold RNA

By performing RNA sequencing (RNA-seq) analysis on the K562-Cas9 cells which infected with genome-scale lentiviral sgRNA library, we want to investigate whether our strategy can be applied in CRISPR screen with single cell transcriptomic readout. RNA-seq analysis showed that we can capture the scaffold RNA together with the endogenous mRNA  precisely. The gene expression profile after genome perturbation can be easily identified together with the perturbation information in single experiment.We performed Single cell RNA-Seq by Smart-seq2/C1 platform for 73 cells. The gRNA scaffold was not detected in five cells, the numbers for these cells are NKC1.8, NKC1.11, NKC1.12, NKC1.27 and NKC1.37. Our framework offered strategies that can be conveniently applied to study the genotype and mRNA profiles after CRISPR-mediated genome perturbation with single-cell transcriptional readout