Extended Data Fig. 9: UDA-seq is compatible with CRISPR Screening. | Nature Methods

Extended Data Fig. 9: UDA-seq is compatible with CRISPR Screening.

From: UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing

Extended Data Fig. 9: UDA-seq is compatible with CRISPR Screening.

a. Pie plot displaying 38000 cells’s sgRNA detection rate. b. Sankey diagram showing sgRNA number distribution out of 31,487 cells. c. Distribution of gene and UMI numbers per cell in single-cell transcriptome (n = 12,644). Box plots show interquartile range with the median marked. The whiskers extend up to 1.5 times the interquartile range, the outliers are not displayed. d. The genes that exhibit differential expression in cells subjected to interference targeting EP300 as compared to those targeted by the negative control sgRNA. P values were calculated by two-sided Wilcoxon Rank Sum test. e. The scMAGeCK-LR module estimated the degree of perturbations of the interested genes (FAR2 in the left panel and NDUFS5 in the right panel). An LR_score >0 represented up-regulation by the corresponding target genes, while an LR_score <0 represented down-regulation. f. PCA analysis showed that cells transduced with negative control sgRNAs were evenly distributed within group 1 and group 2 SUN16 cells. g. The expression of the MYC gene was notably reduced in cells (n = 5) subjected to each interference targeting genes compared to the control (n = 10) in group 2 cells. Box plots show interquartile range with the median marked. The whiskers extend up to 1.5 times the interquartile range.

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