Supplementary Figure 4: Expression profiles of highly variable genes before and after cell-cycle correction and pseudotime ordering of mESC inDrop data

Heatmap displaying the expression profiles of 2047 highly variable genes before a) and after cell-cycle correction and pseudotime ordering (b,c), time courses of gene expression along batch (d) and pseudotime (e,f), GO enrichment analysis of the clusters in (a,c). The colored top bar (a-c) indicates the time after LIF withdrawal (dark blue: day 0, light blue: day 2, yellow: day 4, red: day 7). a) Gene expression with strong day-to-day variability. b) Cell-cycle corrected gene expression and additional quantile normalization. c) Cell-cycle corrected gene expression and additional Z-score normalization. Pseudotemporal ordering is indicated by mixed colors in the top annotation bar. In the time courses, the respective genes are indicated in grey, the black curve is the smoothed mean. d) log-transformed gene expression counts. e) Cell cycle correction, log transformed gene expression counts, quantile normalization (cf. Fig. 2d in main text). f) As in E), with Z-score normalization. All clusters share the same temporal behavior. The green cluster GO terms are not shown. For each cluster, five representative GO terms are displayed. g) GO terms before cell-cycle correction, h) after cell-cycle correction and Z-score normalization. i) Distribution of cells along pseudotime labeled by time after LIF withdrawal.