Fig. 5: Effects of SNORD115 and SNORD116 cluster deletions on transcriptome.
From: Roles of SNORD115 and SNORD116 ncRNA clusters during neuronal differentiation
A Heatmaps representing global changes to the transcriptome in differentiating wild-type and mutant cell lines. Mean expression (CPM) values are scaled for each gene across all the timepoints and all cell lines. B Number of differentially expressed genes between wildtype and mutant cells increases with the progress of differentiation. C Changes to gene expression in mutant vs wildtype cells at day 15 of differentiation, indicating a tendency towards decreased expression. D Hierarchical clustering of RNA-seq samples shows high similarity between undifferentiated cells and subsequent separation between WT and deletion mutant cell lines. E Overlap between differentially expressed genes (DEGs) for H115 and H116 cell lines. F Gene expression profiles of DEGs, show very high similarity between H115 and H116 cell lines. Heatmap covers all 847 DEGs identified independently in both mutant cell lines and at all timepoints. G A summary of the GO term enrichment analysis for H116 DEGs from g::Profiler, using default statistical parameters: Fishers’ one-tailed test and multiple testing correction algorithm g:SCS. Full outcome of the analysis is in the Supplementary Data 4. H PCA analysis of RNA-seq data implies accelerated differentiation of H115 and H116 cells lines along the assumptive differentiation pathway. I Comparison of H116 and WT transcriptomes at D15 of differentiation with transcriptomes of various cell types identified during human mid-brain development (scRNA-seq)41. The mutant cells are more similar to mature neurons relative to the WT. GSEA analysis (see Methods). RGL1-3 radial glia-like cells, PROG progenitor cells, BP basal plate, FPL lateral floorplate, FPM medial floorplate, M midline, NPROG neuronal progenitors, OPC oligodendrocyte precursor cells, NBML1-5 mediolateral neuroblasts, DA-DA2 dopaminergic neurons, OMTN oculomotor and trochlear nucleus, RN red nucleus, SERT serotonergic, MGL microglia. Source data are provided as a Source Data file.
