Extended Data Fig. 5: Quality control, processing and analysis of DMGO scRNA-seq data.
a, Violin plots showing the number of genes, number of counts, percentage mitochondrial genes and percentage of ribosomal genes after filtering on a sample-by-sample basis. Box plots inside violin plots show the median (center line, 50th percentile), the box spans the interquartile range (25th–75th percentiles), whiskers extend to the most extreme observations within 1.5×IQR of the quartiles (defining the plotted minima and maxima). b, Unintegrated UMAP representation of DMGO cells, colored by sequencing batch. c, iCNV profile of DMGO cells showing chromosomal aberrations compared to healthy cells from the BrO time course data shown in Fig. 1e. Orange depicts tumor and green represents healthy cells. d, Dotplot showing marker gene expression for different tumor states, color-coded for their respective annotation. e, Matrixplot with the obtained tumor state annotations compared to reference datasets7,8. f, Mapping scores of DMGO cells in Liu et al.8, showing high presence of the annotated cell states, except for cycling cells. For panels a-f, n = 14 DMGOs from 4 independent batches.
