Evaluation of Large-Scale Single Cell CRISPR Activation Screen

Abstract

The combination of single cell transcriptomics with large-scale CRISPR screening is a powerful approach that enables high throughput characterization of perturbation effect at cellular resolution. While there have been plenty of studies conducted with CRISPR knockout and interference screens, less studies have been conducted with CRISPR activation. Here we conducted multiple CRISPR activation screens with two scRNA-seq platforms, the 10x Chromium 5’ and the PIP-seq. The experiment results demonstrated the technical feasibility of scaled single cell CRISPRa screening and profiled the efficiency of guides from multiple CRISPR activation libraries. Certain guides with strong downstream perturbation effects were identified. The PIP-seq platform exhibited potential as a high throughput and cost effective guide screening approach. Finally, we proposed a refined workflow for single cell CRISPRa screen by combining the PIP-seq and 10x Chromium platform to generate high resolution single cell perturbation data more efficiently.