Extended Data Fig. 4: Comparison of cell-type transcriptomes determined by scRNAseq to data from bulk populations described in literature.
a, Enrichment of gene expression signatures of haematopoietic populations in immune cell transcriptomes published by the ImmGen consortium (data source: GEO GSE109125)58. Data points in the same row correspond to experimental replicates. b, Enrichment of gene expression signatures of non-haematopoietic populations in published transcriptomes of populations defined by genetic markers5,7,8,9,59; see methods for specification of data sources, and see the Supplementary Note 1 for a detailed evaluation of the algorithm used. c, The optimal number of mesenchymal cell clusters was determined using the SOUP method15, a semi-soft clustering algorithm designed to distinguish between distinct cell types and transition states between cell types. Error bars indicate 90% confidence intervals across 10 independent SOUP runs, central values correspond to medians. d, Main cluster identity from SOUP highlighted on the t-SNE from Fig. 1b (mesenchymal cell types only, n=2223 cells). e, Comparison of clusters identified by Seurat (Fig. 1b) to clusters identified by SOUP (panel d) demonstrates strong overlap between both methods.
