Fig. 4: Reanalysis with covariates and singleton experimental validations support and extend results.
From: Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
a Singleton validation results for K562 cells. Categorical heatmap indicating whether a K562 hit gRNA was detected with SCEPTRE, our original approach, targeted a promoter or enhancer, drove K562-specific upregulation, and whether it was validated with singleton experiments. Hit CREs that drove upregulation in singleton validations are labeled and coloured according to target CRE class. b Boxplots displaying the average log2 fold change between cells with a given gRNA (n = 3 independent lines) and controls (n = 21 lines). Normalized expression displayed in transcripts per million (TPM). Boxes represent the 25th, 50th, and 75th percentiles. Whiskers extend from hinge to 1.5 times the inter-quartile range. All data points are also plotted on top of the box plot for transparency. P-values are from a two-tailed Wilcoxon rank-sum test with a significance threshold of 0.1. c Singleton validation results for iPSC-derived neurons. Categorical heatmap indicating whether a neuron hit gRNA was detected with SCEPTRE, our original approach, targeted a promoter or enhancer, drove iPSC-derived neuron-specific upregulation, and whether it was validated with singleton experiments. Hit CREs that drove upregulation in singleton validations are labeled and coloured according to target CRE class. d Boxplots displaying the average log2 fold change between cells with a given gRNA (n = 3 independent lines) and controls (n = 21 lines). Normalized expression displayed in transcripts per million (TPM). P-values as in panel (b). The two instances where expected upregulation was not observed in a particular cell context are labeled in gray above the corresponding box plot (specifically gRNAs targeting e-HMGA1 in K562 cells and a promoter of FOXP1 in neurons). Boxes as in panel (d). The 14/16 experiments where the expected result was observed are labeled in black above the corresponding box plot, while the 2/16 that are labeled in gray failed to validate.
