title: Bulk RNAseq of arthritic mouse: 8 weeks ankle joint - lining synovial fibroblasts
design: RNA was isolated from sorted ankle joints synovial fibroblasts (sublining and lining) of healthy (4 weeks of age) and hTNFtg mice (4 & 8 weeks of age) using the RNeasy mini or micro kit (QIAGEN). The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent. RNA samples with RNA Integrity Number (RIN) > 7 were used for library construction using the 3 mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN). DNA High Sensitivity Kit in the bioanalyzer was used to assess the quantity and quality of libraries (Agilent). Libraries were then pooled and templated using the Ion PI IC 200 Kit (ThermoFisher Scientific) on an Ion Proton Chef Instrument or Ion One Touch System. Sequencing was performed using the Ion PI Sequencing 200 V3 Kit and Ion Proton PI V2 chips (ThermoFisher Scientific) on an Ion ProtonTM System.