Extended Data Fig. 10: Additional Perturb-Seq analysis.
From: Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing
(a) Histogram of the number of guide UMIs per cell from targeted PCR amplification PCR. (b) Histogram of the number of CITE-seq ADT UMIs per cell. (c) Histogram showing the number of guides with a given number of cells assigned to them. Note the y axis is log10 scaled. Dotted line: 10 cells per guide. (d) UMAP of gene expression for Illumina. (e) Feature plot of the number of genes for Illumina. (f) Violin plots of DE genes among clusters in the Illumina data. Shown are clusters showing active cell cycling (cluster 0, 1, and 5) and a cluster with high immediate early gene levels (cluster 5). (g) UMAP of gene expression for Ultima. (h) Feature plot of the number of genes for Ultima. (i) Violin plots of DE genes among clusters in the Ultima data. (j) Scatterplot of -log10 (p-value) for each guide/gene pair in Illumina vs. Ultima, where the p-values are the output of DE analysis comparing each guide to the control Intergenic_1 guide. (k) Scatterplot of logFC for each guide/gene pair as in (j). Only gene/guide pairs with uncorrected p-value < 0.01 in either Ultima or Illumina are shown.
