title: scATAC-seq of arthritic mouse: 4 weeks ankle joint - synovial fibroblasts
design: Sorted live Pdpn+ CD45- CD31- Ter119- synovial cells of hind paws of Tg197 mice at the age of 4 weeks were subjected to 10X Genomics Single Cell ATAC Kit version 2. Nuclei were resuspended in 1x Diluted Nuclei Buffer (10x Genomics). Transposition was performed at 37 for 60 mins. Generation of Gel beads in EMulsions (GEMs) using Chromium Controller (10x Genomics), was followed by GEMs incubation and cleanup, based on 10x Genomics recommendations. Amplification of libraries was performed in a Veriti Thermal Cycler (Thermo Fisher) programmed at 98  for 45 s followed by 12 cycles of (98  for 15 s, 67  for 30 s, 72  for 20 s), 72  for 1 min and hold at 4 . In turn, libraries were double sided size selected using SPRI select reagent (Beckman Coulter) according to 10x Genomics recommendations. Before multiplexing, libraries were assayed on Bioanalyzer High Sensitivity DNA ChIP (Agilent), for quality check and determination of fragment size. Quantification of libraries was performed using Qubit dsDNA HS Assay Kit (Thermo Fisher, Cat. No Q32851). Next generation sequencing was performed at EMBL-Genecore (Heidelberg), using the NextSeq 500 platform for paired-end 75 bp reads.