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single cell crispr screening

Single-Cell CRISPR Screening CapitalBio

Traditional CRISPR screening is to first construct a mixed sgRNA library, which can contain hundreds to thousands of sgRNAs, and then transfect the library into cells that can stably express Cas9 protein to achieve large-scale gene knockout. Cells are subjected to phenotype screening and bulk sequencing to obtain information on sgRNA changes during the culture process, so as to know the impact of the knocked-out gene on the cells. This conventional method can only screen macroscopic phenotypes of cells, so it is more suitable for answering questions directly related to cell survival or macroscopic phenotypes, but not suitable for research on molecular phenotype changes. Based on this, 10x Genomics has developed a single-cell CRISPR screening platform, which uses high-throughput single-cell sequencing to obtain the gene expression profile and sgRNA expression of a single cell from the cells screened by CRISPR. The results of the CRISPR screen were tested at the level of phenotype.

Method Applications Analysis Display


Figure 1. Single Cell CRISPR Screening Workflow


Figure 2. Single Cell CRISPR Principles

  • Functional Genomics Research

  • Tumor Mechanism Research

  • Drug Target Screening

  • Immune Regulation Mechanism

  • Stem Cell Regulatory Research

  • Infectious Disease Research


Grouping plot by sgRNA


Target gene expression violin plot


Correlation heatmap between sgRNA subgroups


Dimensionality reduction visualization of sgRNA subgroups by phenotype


Density and contour plots of the expression of the specified sgRNA target genes in the UMAP plot


Heatmap of correlation between sgRNA subgroups and gene expression subgroups


sgRNA subgroup calculation boxplot of a gene set score


Transcriptome subgroup marker gene heatmap and list of significantly associated sgRNA target genes

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