Figure 6. Single-cell information reveals a bifurcated UPR within a population and allows unbiased discovery of UPR-controlled genes.
(A) Single-cell projections (t-sne) of sgRNA identity, cell cycle position, and UMI count per cell in HSPA5-perturbed and control cells (containing the NegCtrl-3 guide). We note that the HSPA5-targeting sgRNAs indicated differ by only 1-nt (Table S1).
(B) LRICA analysis of HSPA5-perturbed cells identifies two subpopulation-defining independent components. Right panel: subpopulations defined by thresholding IC1.
(C) Branch activation scores in HSPA5-perturbed cells.
(D) Normalized expression of UPR genes in HSPA5-perturbed cells. Each row is a cell, ordered by increasing IC1, and each column is a gene in the same order as Figure 3F.
(E) Mean expression of HSPA5 across subpopulations. Error bars are 95% CI.
(F) Cell cycle composition of HSPA5-perturbed cells.
(G) Strategy for using correlated expression to identify functionally related genes.
(H) Unbiased identification of induced gene expression programs. Top: Normalized expression of 200 genes with significantly altered expression in UPR Perturb-seq experiment clustered based on co-expression. Bottom: Normalized expression in UPR epistasis experiment, to assess UPR dependence. Full version in Figure S6A.
(I) UPR-responsive genes with altered expression in the UPR Perturb-seq experiment clustered by co-expression in the UPR epistasis experiment, the UPR Perturb-seq experiment, and control cells. Cophenetic correlation coefficients between dendrograms along with a visual guide to the movement of major groups included. Full version in Figure S6B.
(J) Strategy for enriching cells perturbed for a trait of interest.
(K). Within cells enriched for a set of bait cholesterol biosynthesis genes, a group of genes clustered with the bait genes and had more correlated expression than in control cells. Reactome annotations and SREBP binding data for the group included (right panel).
See also Figure S6.