Figure S1. Batch characterization.

Batch characteristics across nine different batches related to differences between patients, media storage, and use of sequencing protocols (batch origin). The following characteristics are shown: mean per cent variance associated with the batch variable across all genes (PVE_batch), mean per cent variance associated with the cell-type variable across all genes (PVE_celltype), mean relative number of differentially expressed genes between batches (DE_genes), mean Pearson correlation of log fold changes of the batch effect between cell types (lfc_correlation), mean overlap of DE genes between different cell-types (de_overlap).