Fig. 3: GL261 cells undergo transcriptional changes under different conditions. | Communications Biology

Fig. 3: GL261 cells undergo transcriptional changes under different conditions.

From: Single-nucleus RNA sequencing reveals a preclinical model for the most common subtype of glioblastoma

Fig. 3

A PCA visualization of malignant cells, colored by cell type. k = 16,757 individual cells. B Heatmap showing relative expression of each of the 50 top expressed genes in each culture type. Columns correspond to cultured GL261 and GL261-GSCs and implanted GL261-GSCs. Selected genes are indicated (see Table S4 for the full list). C Top 10 enriched terms from gene ontology (GO) gene sets in cultured GL261 and GL261-GSCs and implanted GL261-GSCs compared to the others (see Tables S5–S7 for full lists). D Heatmap showing the meta-module scores described by Neftel et al.6 E Two-dimensional representation of the cellular states described by Neftel et al.6 for each group. Each quadrant corresponds to one cellular state and each dot represents a cell. F Barplot showing the percentage of cycling cells analyzed, calculated as the sum of percentages of S and G2/M phases, in GL261, GL261-GSCs and implanted GL261-GSCs (Suppl. Fig. 3B). G Venn diagram showing the overlap between differentially expressed genes across different types. Plotted data are provided in tabular form in Table S7. Differential gene expression was analyzed using Wilcoxon test with a p-value cutoff=0.05. H Illustrative Sox6 immunofluorescence images of brains at 28 days post-implantation showing that transplanted tumor cells express Sox6, scale bar: 2 mm. Lower panels: zoomed-in images showing tumor cells at the border of the tumor containing different levels of the transcription factor Sox6, scale bar: 100 µm. Quantification of Sox6 protein levels in the tumor area and contralateral hemisphere from the immunofluorescence images. Results are expressed in arbitrary units (a. u.) and are the mean±SEM from three independent experiments from which 5 fields were quantified. ***P < 0.001 (student’s t test). I Sox6 protein levels in the contralateral region and tumor area detected by western blotting (representative blots). GAPDH is shown as loading control. Full-length Western blots are shown in Suppl. Fig. 7A.

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