Expression of cell-type-cluster-specific genes in GTEx organs. (A) Enrichment of each major cell type in GTEx tissues, estimated from bulk tissue RNA-seq using the xCell method. As a control, we also include, at the bottom of the plot, the enrichments of the endothelial, epithelial, and mesenchymal primary cells monitored here (Fig. 1B). As expected, since the gene signatures have been derived from these very same cells, endothelial primary cells are heavily enriched in the endothelial type, but not in the other types, epithelial cells in the epithelial type and mesenchymal cells in the mesenchymal type. (B) Example of stomach histological slides, which represent the two main tissue layers and the procedure for the manual annotation of the images based on the presence of those layers. Each GTEx histological image displays up to six tissue slices. For the stomach samples, we scored each slice for the presence (1) or absence (0) of the muscularis and mucosa layers, summed up the values for each layer separately and divided by the number of slices. If the proportion of slices with mucosa layer, or muscularis layer, is more than 50% we classify the entire slide as mc1, or ms1, respectively. If the proportion is lower, we classify the slide as mc0 or ms0. A combined class, for example mc0ms1, is assigned to the slides. Thus, samples labeled mc0ms1 are mostly muscularis, and samples labeled mc1ms0 are mostly mucosa. (C) Enrichment of cells of epithelial and mesenchymal types in stomach samples containing mostly the mucosa (green) or mostly the muscularis (purple) layer. (D) Expression of the cell-type-specific genes that drive the separation of stomach samples in mostly muscularis or mostly mucosa samples. Among discriminant cell-type-specific genes, mucosa-only samples express almost exclusively epithelial-specific genes, whereas muscularis-only samples express exclusively mesenchymal-specific genes.
