10x single cell ATAC library generated from an osteoarthritis synovial tissue sample.
Each osteoarthritis synovial tissue sample was processed separately in the cell capture step. Nuclei were isolated using an adaptation of the manufacturer's protocol (10X Genomics). Approximately ten thousand nuclei were incubated with Tn5 Transposase. The transposed nuclei were then loaded on a Chromium Next GEM Chip H and partitioned into Gel Beads in-emulsion (GEMs), followed by GEM incubation and library generation. The ATAC libraries were sequenced to an average of 30,000 reads per cell with the recommended number of cycles according to the manufacturer's protocol (Single Cell ATAC V1.1, 10X Genomics) using Illumina Novaseq. Samples were initially processed using 10x Genomics Cell Ranger ATAC 1.1.0, which includes barcode processing and read alignment to hg38 reference genome.