title: scRNA-seq of arthritic mouse: 8 weeks ankle joint - synovial fibroblasts
design: Sorted live Pdpn+ CD45- CD31- Ter119- synovial cells of hind paws of Tg197 mice at the age of 8 weeks were subjected to 10X Chromium Single Cell 3 Solution v3. After encapsulation, emulsions were transferred to a thermal cycler for RT. cDNA was purified and amplified with primers provided in the Single Cell 3 reagents (10X Genomics). After purification with 0.6X SPRIselect beads (Beckman Coulter) cDNA quality and yield was evaluated using an Agilent Bionalyzer 2100. Using the provided enzyme fragmentation mix the libraries were fragmented, end-repaired and A-tailed. Products were cleaned using SPRIselect beads and adaptors provided in the kit were ligated. After cleaning ligation products, libraries were amplified and indexed with unique sample index i7 trough PCR amplification. Final libraries were double sided cleaned and their quality and size was evaluated using an Agilent Bioanalyzer 2100. Libraries were sequenced on Illumina NextSeq 500 sequencer.