Extended Data Fig. 3: Single-cell RNA-seq reveals main trajectories of WT and K36M reprogramming intermediates.
From: H3K36 methylation maintains cell identity by regulating opposing lineage programmes
(a) UMAP embedding of scRNA-seq data (Seurat framework) using MEFs, reprogramming intermediates on days 2, 4, 6, 8 for WT and K36M, as well as passaged iPSCs. For each indicated group, one sample was encapsulated leading to n = 38,743 cells total. (b) Expression of pluripotency gene Nanog projected on the same UMAP embedding as in (a). (c) Expression of mesenchymal gene Prrx1 projected on the same UMAP embedding as in (a). (d,e) Diffusion pseudotime mapping of day 2 to day 8 intermediates undergoing reprogramming. WT cells are colored in blue, K36M cells in red. (f) Expression of pluripotency gene Nanog projected on the same pseudotime embedding as in (d). (g) Expression of epithelial gene Cdh1 projected on the same pseudotime embedding as in (d). (h) Expression of mesenchymal gene Zeb1 projected on the same pseudotime embedding as in (d). (i) Relative expression (RNA-seq) of mesenchymal and epithelial genes in MEFs expressing H3.3 WT or K36M, but not OKSM, n = 2 biologically independent experiments. (j) Gene ontology terms of genes downregulated in K36M MEFs without OKSM. Analysis and p values from geneontology.org. (k) Gene ontology terms of genes upregulated in K36M MEFs without OKSM. Analysis and p values from geneontology.org.
