Extended Data Fig. 7: Silencing MAT2a alters the transcriptome and H3K36me3 deposition.
A. Volcano plot of differential gene expression comparing MAT2A knockdown to control DIPG04 cells. Canonical neuronal markers are highlighted in red (designating up-regulated genes) or blue (designating down-regulated genes). Statistical adjustments were made for multiple comparisons using iDEP.94 DESeq2 Statistical packages in R. B. Top 10 Gene sets, (Gene Ontology), derived from GSEA analysis of changes to the transcriptome in MAT2A knockdown. C. Heatmap of top 10 negative and positive enriching developmental cell signatures in MAT2A knockdown. D. Enrichment plots of selected developmental cell signatures from Extended Data Fig. 7C. E. Realtime PCR validation of selected canonical neurogenesis genes and markers of oligodendrocyte cells. Experiment was performed one time, n=3 technical triplicates for each gene. F. Heatmap of spike-in normalized H3K36me3 ChIP-Rx-seq reads centered at human genes in no doxycycline (top panel) vs. doxycycline (bottom panel) induction of MAT2A shRNA expression in DIPG04 cells. G. Bar plots of H3K36me3 ChIP-Rx-seq reads demonstrating alterations of H3K36me3 at different regions summarized across all human genes in DIPG04 cells. H. Venn diagram of overlapping genes between ChIP-Rx-seq and RNA-seq data. I. Plot of H3K36me3 (fold-change) vs. RNA seq (fold-change) with MAT2A KD, neurogenesis makers are indicated.
