Extended Data Fig. 6: Multi-omics factor analysis reveals coordinated epigenetic and transcriptomic variation during endothelial-to-hematopoietic transition between YS and AGM.
a, The variance explained by DNA and RNA profiles of CoTECH experiments for all AGM cells. b, Scatter plot of MOFA factor 1 (x axis) and MOFA factor 2 (y axis) for all AGM cells. Cells are colored as in Fig. 6. c, UMAP visualization of expression of marker genes for AGM cells. d, The variance explained by DNA and RNA profiles of CoTECH experiments for all YS cells. e, Scatter plot of MOFA factor 1 (x axis) and MOFA factor 2 (y axis) for all YS cells. Cells are colored as in Fig. 6. f, UMAP visualization of expression of marker genes for YS cells. g, Heatmaps showing RNA (left) and H3K27ac (right) signals at gene-correlated peaks in AGM cells along the pseudotime during EHT. The rows represent 2,219 non-differential genes. h, Line plots showing average RNA and H3K27ac signals of three gene clusters ranked by gene expression levels as in (g). i, Heatmaps showing RNA (left) and H3K27ac (right) signals at gene-correlated peaks in YS cells along the pseudotime during EHT. The rows represent 2,008 non-differential genes. j, Line plots showing average RNA, H3K27ac signals of three gene clusters ranked by gene expression levels as in (i). k-l, Heatmaps showing the TF motif scores calculated using chromVAR with default parameters (g) and gene expression (j) during AGM-EHT. i-j, Heatmaps showing the TF motif scores calculated using chromVAR with default parameters (i) and gene expression (j) during YS-EHT. k, Inferred enhancer-to-target links for Runx1 in YS-EC, YS-HEC, AGM-earlyEC, and AGM-HEC. The enhancer-to-gene relationships were computed using enhancerToGene function in ScoMAP, and the links were plotted by Cicero.
