Supplementary Figure 8: Bulk RNA-seq analysis for the arrayed validation screen | Nature Methods

Supplementary Figure 8: Bulk RNA-seq analysis for the arrayed validation screen

From: Pooled CRISPR screening with single-cell transcriptome readout

Supplementary Figure 8

a) Hierarchical clustering of the median expression of TCR activation signature genes, based on bulk RNA-seq data aggregated across gRNAs for the same target gene. Clustering of rows and columns used the Pearson correlation, and z-scores of expression are shown. b) Correlation (row-wise z-score) of bulk RNA-seq transcriptomes with a matrix comprising synthetic mixtures of transcriptome profiles between the median of non-targeted cells in both conditions (values close to one reflect similarity with anti-CD3/CD28 stimulated cells). Additional metrics are shown as columns (center) and reveal no relationship with the inferred position of the corresponding samples. The effect that perturbing each target gene had on the TCR activation signature based on the bulk RNA-seq data was assessed in comparison to the control group (barplot on the right). c) Correlation (top) of median expression levels based on CROP-seq aggregating across target genes (left) or gRNAs (right) compared to the respective bulk RNA-seq libraries across all TCR activation signature genes. The corresponding number of cells in each group is shown at the bottom. Empty values reflect lack of matching bulk RNAseq libraries due to failed samples in the bulk RNA-seq. d) Comparison of the signatures inferred from CROP-seq (x-axis) with those derived from bulk RNA-seq data (y-axis) across all shared gRNAs. e) Comparison of the relative impact of each gRNA (left) or target gene (right) on the TCR activation signature relative to the corresponding control for CROP-seq (x-axis) and bulk RNA-seq (y-axis).

Back to article page