Single cell RNA-seq of human synovial joints from healthy donors

Human synovial Single cell RNA-seq was performed on three tissue samples from healthy donors. This experiment was done to explore the heterogeneity of cells in healthy human synovial joint and enabled the comparison of cellular states and composition to those of publicly available single cell RNA-seq datasets from psoriatic arthritis and rheumatoid arthritis patients. Human synovial cells were loaded immediately after tissue dissociation with up to 25,000 cells in a single well of a Chromium chip G (10x Genomics). 3' gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as paired end (PE) 150 bp by Illumina sequencing to 65-80% saturation. Reads were mapped to the GRCh38 human genome (GENCODE) using the 10x Genomics Cell Ranger pipeline (7.2.0).