Figure 3

Major9 cell type profiles. (a,b) The first two principal components of the pseudo-bulk expression profiles of the Major9 cell types before normalization colored by sequencing platforms of the source datasets (a) and by cell types (b) showed the samples grouping by sequencing platforms. (c) After ComBat normalization across all datasets, cell type information was lost. (d) After ComBat normalization separately on each cell type, the pseudo-bulk samples grouped by cell types, as expected. (e) Expression profiles of all genes in the pure pseudo-bulk samples. (f) A subset of profile genes was selected such that their expression levels were comparable across cell types. The numbers next to the cell type labels indicate the number of genes in each of the cell type profiles. (g) The expression of the profile genes was higher in their respective cell type compared to all other types. Inkscape v1.0.2 (https://inkscape.org/) was used to assemble the figure.