Single-cell RNA-seq of Mesenchymal Cells

Single-cell library preparation was performed using Chromium Single Cell 3′ GEM Library & Gel Bead Kit v3 (cat. no. 1000092, 10x Genomics) according to manufacturer’s instruction. The libraries were sequenced on the NextSeq 500 system (Illumina) using the NextSeq 500/550 High Output kits v.2.5 (50 cycles; cat. no. FC-404-2005, Illumina). The sequencing outputs were processed using the CellRanger software v.3.1.0 on the GHPCC. Reads were mapped to human reference genome GRCh38 (Ensembl 93). Data analysis was performed using Seurat v.4.1.0 (ref. ^{60 (link)}) within R v.4.0.2 environment. RNA velocity analysis was performed using the velocyto v.0.17 commend line tool and velocyto.R v.0.6 R package^{61 (link)}. Sequencing results have been deposited in the Gene Expression Omnibus (accession no. GSE198482) and analysis scripts are available at https://github.com/zingery/mesenchymal-maintenance/.