Extended Data Figure 6: Cell-cycle analysis.

a, High expression of G1/S and G2/M gene sets in a subset of cycling cells. Shown are the average expression (top panels, lines) or the expression of all individual genes (bottom, heat maps) of the G1/S and G2/M gene sets, in all cells (n = 2,594) (left) or only among the putative cycling cells (n = 119) (right) from the three tumours profiled at high-depth ordered by cell cycle expression. Dashed lines (top right) separates the four inferred phases of cycling cells, corresponding to light blue, blue, green and red in Fig. 3a, respectively. b, Estimated fraction of cycling cells (y axis) in each of 3 tumours (x axis) based on single cell RNA-seq (left; different phases marked by colour code as in Fig. 3a) or Ki-67 immunohistochemistry (right). c, Variation in cycling cells between regions of the same tumour. Shown is Ki-67 immunohistochemistry in two regions in MGH36. Such regional variability in proliferation complicates direct comparisons as done in b. d, Cycling cells are enriched in stem-like and undifferentiated cells compared to differentiated cells. Shown is the percentage of cycling cells (y axis) in four bins based on stemness scores (top) or lineage scores (bottom). Black squares and error-bars correspond to the mean and standard deviation of the percentages in the three tumours profiled at high depth (MGH36, MGH53, MGH54), and red circles denote the percentages in individual tumours. Bins in left panel were defined as stemness scores below −1.5 (n = 711), between −1.5 and 0.5 (n = 1,100), between −0.5 and 0.5 (n = 939), and above 0.5 (n = 274), respectively. The first two bins are significantly depleted with cycling cells, while the last two bins are significantly enriched (P < 0.05, hypergeometric test). Bins in left panel were defined as AC score above 1 (n = 503), AC score between 0.5 and 1 (n = 1,013), AC and OC scores below 0.5 (n = 1,130), OC score between 0.5 and 1 (n = 855), and OC score above 1 (n = 597), respectively. The third bin is significantly enriched with cycling cells, while the four other bins are significantly depleted (P < 0.05, hypergeometric test). e, Correlation between the average expression of cell cycle (y axis) and that of stemness genes (x axis) across molecularly defined oligodendrogliomas (by IDH mutation, chromosome 1p and 19q co-deletion, and absence of P53 and ATRX mutations) profiled by TCGA (n = 69) with bulk RNA-seq. Average expression was defined by centring the log₂-transformed RSEM gene quantifications. Also shown are the linear least-square regression and Pearson correlation coefficient. f, Specific enrichment of S/G2/M cells compared to G1 cells among stem-like or undifferentiated cells. Shown is the proportion (y axis) of each marked category of cells among the stem-like or undifferentiated subpopulations. Significant enrichments are marked (P < 0.01, hypergeometric test).