Fig. S1

Genome-wide expression of retrotransposons in OPC and OL, related to Figure 1 (A) Dendrogram representation of OPC and OL samples, showing OPC and OL samples were formed two separate clusters. Average linkage hierarchical clustering (using Euclidean distance matrix) was performed with respect to the intensity levels of probes in Affymetrix GeneChip. (B) Probe level analysis of differential expression. Differentially expressed retrotransposons probes (red and green dots) and probes for protein-coding genes (gray dots). Probes for which the expression difference between OL and OPC is 2-fold up or down and the adjusted p < 0.05 were considered differentially expressed. FC, fold change; p adj, adjusted p value (Benjamini-Hochberg FDR). (C) Left: heatmap plot and dendrogram representation of all differentially expressed probes in OL and OPC samples. Right: differential gene expression (log2 value) of retrotransposon probes were plotted. UP: induced probes, DOWN: repressed probes. Proportion of different retrotransposon type in induced and repressed probes were plotted in a pie chart. (D) Probability density plots showing the behavior of retrotransposon probes, non-retrotransposon probes, all probes and differentially expressed retrotransposon probes. Vertical dotted lines: 2-fold change of expression. ∗p < 0.05, Wilcoxon rank sum test. (E) Expression levels of RNLTR12-int and myelination hubs were represented as a heatmap and a dendrogram derived after two-way hierarchical clustering.