Cells from each of the 40 sequencing pools (23 from the single-cell multiome assay and 17 from the single-nuclei RNA-seq assay) were demultiplexed back into their samples of origin using the tool Demuxlet93 with default parameters, which uses genotype variant information for each sample to predict the sample of origin for each cell barcode, as well as identify doublet cells, artifactual libraries generated when two cells are captured in the same droplet during library preparation. Between 55% and 75% of cells from each pool were identified as singlets and assigned to a sample. The remaining cells (identified as doublets or ambiguous) were removed from further analysis.
