Fig. 8: Cells responded differently under hypoxia.
From: Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines
a The subclusters could be matched before and after hypoxia treatment in ZR-75-1. Left, UMAP plots scRNA-seq of ZR-75-1 before hypoxia treatment. Middle, UMAP plots scRNA-seq of ZR-75-1 upon hypoxia treatment. Right, the barplot shows the abundance of clusters in ZR-75-1 with or without hypoxia treatment. Different clusters are labeled with different colors. b Volcano plot showing log2 fold change (x-axis) and −log10-transformed FDR-adjusted P-value (y-axis) of differentially expressed genes in corresponding clusters of ZR-75-1 between control and hypoxia treatment (n = 83 DEGs in corresponding cluster 0 of ZR-75-1 between control and hypoxia, n = 182 DEGs in corresponding cluster 1 of ZR-75-1 between control and hypoxia, n = 144 DEGs in corresponding cluster 2 of ZR-75-1 between control and hypoxia). A moderated t-statistics and empirical Bayes methods was used to test statistical significance. Upregulated genes are shown in red, and downregulated genes are highlighted in blue. Insignificant genes are colored in gray. c Cells in the same subcluster responded differently to hypoxia in DLD-1. Left, UMAP plots scRNA-seq of DLD-1 before hypoxia treatment. Middle, UMAP plots scRNA-seq of DLD-1 upon hypoxia treatment. Right, the barplot shows the abundance of clusters in DLD-1 with or without hypoxia treatment. Different clusters are labeled with different colors. d Volcano plot showing log2 fold change (x-axis) and −log10-transformed FDR-adjusted P-value (y-axis) of differentially expressed genes in corresponding clusters of DLD-1 between control and hypoxia treatment (n = 337 DEGs between cluster 0 and 0-1, n = 422 DEGs between cluster 0 and 0-2, n = 332 DEGs in corresponding cluster 1 of DLD-1 between control and hypoxia). A moderated t-statistics and empirical Bayes methods was used to test statistical significance. Upregulated genes are shown in red, and downregulated genes are highlighted in blue. Insignificant genes are colored in gray. e Cells in one subcluster responded differently to hypoxia in SW620. Left, UMAP plots scRNA-seq of SW620 before hypoxia treatment. Middle, UMAP plots scRNA-seq of SW620 upon hypoxia treatment. Right, the barplot shows the abundance of clusters in SW620 with or without hypoxia treatment. Different clusters are labeled with different colors. f Functional enrichment analysis of differentially expressed genes in subclusters of SW620 between control and hypoxia treatment (n = 93 DEGs between 0 and 0-1, n = 190 DEGs between 0 and 0-2). A one-tailed hypergeometric test was used to test the statistical significance. EMT-related genes were differentially induced by hypoxia treatment in one subcluster of SW620. Source data are provided in the Source Data file.
