Extended Data Fig. 1: Analysis of immune cells of CRC patients and healthy donors.

a, UMAP plots showing 208,004 B lineage cells. Cells are color labeled with their inferred cell types/states based on transcriptional profiles (left) and antibody isotypes using scBCR-seq data (right). b, Bubble plots showing the expression of selected marker genes for B cells subtypes as defined in (a). Dot size indicates frequencies of expressing cells, colored according to average expression levels. c, UMAP plots showing subtypes of myeloid lineage cells. d, Bubble plot showing the expression of select marker genes for myeloid cells subtypes as defined in (c). Dot size indicates frequencies of expressing cells, colored according to average expression levels. e, The same UMAP as in Fig. 1b but with cells color coded by their BCR (left) and TCR (right) expression. f, UMAP plot showing all the T cells colored by 6 subtypes. g, Bubble plots showing average expression levels and proportions of select marker genes for different tissues (upper) and T cells subtypes as defined in (f) (bottom). Dot size indicates frequencies of expressing cells, colored according to normalized average expression levels. h, Heatmap displaying the fraction of T cells subtypes across multiple tissues. i, UMAP plots displaying the expression of CD160 for T cells from ileum (upper), colon (middle) and tumor (bottom).