Additional file 4: of Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

Estimated chromosome copy number analysis in GliNS2 CSCs and CB660 NSCs. a, The distribution of average normalized expression across cells (left) and the distribution of the total normalized counts of the 6350 genes across cells (right). The red line indicates the threshold used to filter out the unqualified genes or cells for estimated chromosome copy number analysis. b, Heatmap of shuffled ECN for all chromosomes (columns) in single CB660 NSCs and GliNS2 CSCs (rows). On the scale, ECN = 0 indicates diploid gene expression levels. The column adjacent to the heatmap shows the cell cycle phase of each cell as determined in Fig. 1b with the color of the bar corresponding to the predicted cell cycle phase. c, Quantification of chromosomal instability for shuffled ECN analysis in CB660 NSCs and GliNS2 CSCs. Bar, median; box 25th to 75th percentile; whiskers, minimum and maximum. P > 0.05; Mann-Whitney U test comparing CB660 NSCs and GliNS2 CSCs. d, Heatmap of ECN for all chromosomes (columns) in single GliNS2 CSCs (rows) using average gene expression in GliNS2 CSCs as the reference. On the scale, ECN = 0 indicates diploid gene expression levels. The column adjacent to the heatmap shows the cell cycle phase of each cell as determined in Fig. 1b with the color of the bar corresponding to the predicted cell cycle phase. (TIF 13786 kb)