Extended Data Fig. 9: Analysis of scMulTI-Tag changes across pseudotime.
From: Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag
a) Violin plots describing H3K27me3 (red), H3K4me1 (orange), and H3K36me3 (teal) single cell MulTI-Tag enrichment in genes that decline in expression as defined by RNA-seq44 during differentiation from hESCs to mesoderm (top, n = 29), endoderm (middle, n = 20), or ectoderm (bottom, n = 19). Enrichment is partitioned by pseudotime quartile (1=lowest, 4=highest). P-values of Wilcoxon Rank Sum test between quartile 1 and all other quartiles for each target are displayed above violins. b) Violin plots describing same as a) for genes that increase in expression as defined by RNA-seq44 . Mesoderm n = 54, Endoderm n = 35, Ectoderm n = 36. P-values less than 0.05 are highlighted in red. c) Heatmaps describing co-occurrence of MulTI-tag targets in selected genes of interest whose RNA-seq expression increases (top) or decreases (bottom) during differentiation from hESC to endoderm in 3626 single cells classified as hESC or different stages of differentiated mesoderm. Heatmaps are sorted left-to-right by increasing pseudotime in the mesendoderm/endoderm trajectory. The balance of enrichment between H3K4me1/H3K36me3 and H3K27me3 in each cell is denoted by color, and the total normalized counts in each cell are denoted by the transparency shading. d) Same as c) for ectoderm trajectory.
