scRNAseq libraries were generated with the Chromium Single Cell 3′ v2 assay (10× Genomics). Samples were diluted for an expected cell recovery population of 5000 cells per lane. Libraries were sequenced on the HiSeq4000 platform (Illumina) to a depth of 160 to 220 million reads per library. Read 1 sequencing was 26 base pairs (bp) long, and read 2 sequencing was 98 bp long. FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded. Downstream processing was conducted with zUMIs v0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample. Ensembl GRCm38 release 92, Ensembl Rnor6.0 release 92, Ensembl Sscrofa11.1 release 92, and Ensembl GRCh38 release 91 were used to align the mouse, rat, pig, and human data, respectively.

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