Fig. 3

Mixing HLA-mismatched PBMCs does not cause allogenic response during multiplexed scRNA-seq sample preparation. a Sample classification results plotted as densities in PBMC gene expression space (top left) grouped according to unmixed donor A PBMCs (bottom left), mixed Donor A PBMCs (bottom right), and Donors A-C PBMCs (top right). b Expression of genes known to be upregulated (e.g., IFNG and CD40LG) or downregulated (e.g., DUSP1 and FOS) by CD4+ T lymphocytes during an allogenic response across unmixed (black) and mixed (red) donor A CD4+ T cell subsets. c Representative CD4+ T cell, CD8+ T cell, CD14+ monocyte, CD16+ monocyte, and NK cell gene expression embeddings following iterative subsetting to select equal numbers from each JSD comparison group. Cells are colored according to donor ID (e.g., a, b, c) and mixing status (e.g., − = unmixed, + = mixed). n = 1336 CD4+ T cells, 448 CD8+ T cells, 864 CD14+ monocytes, 136 CD16+ monocytes, and 224 NK cells. d JSD analysis summary. Bar plots denote average JSD between PBMC donors (white), mixed/unmixed donor A cells (beige), technical replicates (gray), and donor A cells following label permutation (red). Difference in JSD scores between mixed/unmixed and technical replicates depicted in black. Error bars denote +/− 1 standard deviation. n = 100 iterations