Extended Data Fig. 6: Barcode representation after quality control and filtering and cNMF program annotation.
a, Schematic representation of the applied approach for simultaneously recovering transcriptomic information, HTO hashtags and lineage barcodes from DMGOs on a single cell level. A nested PCR strategy was applied for the TrackerSeq barcode. b–f, Quality control assessment and filters used to select barcodes from experimental replicate 1 (top) and experimental replicate 2 (bottom). Histogram depicting the total number of UMI counts prior to any filtering (b). Histogram displaying read counts and the cut-off (red dashed line) set as a minimum total read count of log102 and log103 for experimental replicate 1 and 2, respectively (c). Scatter plot depicting read counts plotted against UMI counts and the applied threshold for minimum total read counts indicated (red dashed line) (d). Histogram depicting the mean oversequence per barcode and thresholding applied (dashed blue line) (e). Scatter plot depicting read counts plotted against max mean oversequence showing both thresholds applied (f). g, UMAP embedding of lineage-traced DMGOs and BrO controls. Cells are colored according to unique lineage barcodes. Cells without barcodes are presented in gray. h, Representation of each DMGO and BrO control in the final UMAP embedding. i, Bargraph depicting the total number of cells for each clonal barcode after applying the filtering of >3 cells per clonal family. j, Pie charts of the relative size of each recovered clonal family among all barcoded cells per sample used for the large versus small clone comparison. Percentage is depicted for clonal families that are equal to, or above 20%, which are defined as large clones. For panel b-j, n = 14 DMGOs and n = 2 BrOs, see Supplementary Table S1 for details. k, Dotplot showing normalized expression of AQP1 and AQP4 in DMG cells7. In contrast to AQP1, AQP4 - a canonical AC-like marker - was present in DMG tumors across all locations. l. Module scores of gene programs as derived from cNMF projected onto the UMAP of lineage-traced cells. m, Heatmap of Jaccard index scores, indicating the overlap of the cNMF derived programs to tumor state annotations. For panels b-j, l, m, n = 14 DMGOs and n = 2 BrOs, see Supplementary Table S1 for details. For panel l and m, n = 14 DMGOs and n = 2 BrOs, see Supplementary Table S1 for details.
