Multi-omic analysis based on MitoSort-identified depletion of B cells in RTX-treated patients
A. Schematic of experimental design. PBMCs from four normal individuals and four patients with autoimmune diseases were collected and pooled. Next, B cells were enriched to profile gene expression, chromatin accessibility, and mtDNA. B. Heatmap showing the allele frequency of aggregated sample-specific mitochondrial germline mutations (rows) across cells (columns) sorted by MitoSort assignment. The number in the parenthesis of each row name represents the number of sample-specific mitochondrial germline mutations for this sample. C. and D. t-SNE plots of cell barcodes based on sample-specific mitochondrial germline variant profiles obtained from MitoSort (C) and mitoSplitter (D). Each dot represents a cell barcode and is colored by the cell classification of MitoSort (C) or mitoSplitter (D). E. PCA plot of the normalized cell-by-cluster log-likelihood matrix from Souporcell. Each dot represents a cell barcode and is colored by the cell classification of Souporcell. F. and G. Percentage of barcodes shared between Souporcell-based and MitoSort-based (F) or mitoSplitter-based (G) assignments in multiplexed multi-omic data consisting of eight donors. H. Bar plot showing the accuracy of cell donor assignment using different methods. Accuracy for each method is computed by considering Souporcell-based donor assignment as true labels. I. Runtime of different demultiplexing methods. J. UMAP of WNN graph for RNA and ATAC-seq modalities showing cell type annotation for each cell. K. UMAP of WNN graph for RNA and ATAC-seq modalities showing cells per individual colored by cell number densities. Disease status and clinical information for each individual are shown in subtitles. L. Bar plot showing the percentage of each cell cluster in each individual. RTX, rituximab; PBMC, peripheral blood mononuclear cell; PCA, principal component analysis; PC, principal component; UMAP, Uniform Manifold Approximation and Projection; WNN, weighted-nearest neighbor.
