title: Day_10_Il6_12_S10
organism: Mus musculus
description: Protocols: Studies of antigen-induced arthritis (AIA) were conducted under UK Home Office approvals (PPL-30/1820; PPL-30/2928; PB3E4EE13; PF34A3DC8; PE8BCF782). Mice were challenged (s.c.) with methylated BSA (mBSA; 1 mg/ml emulsified in Complete Freund's Adjuvant) and 160 ng Bordetella pertussis toxin (i.p.). Following an antigen boost with mBSA and CFA (s.c.), inflammatory arthritis was established by intra-articular (i.a.) administration of mBSA (10μl; 10 mg/ml) into the right knee joint.  Synovial tissues were harvested on days 3 and 10 of AIA. Genomic DNA was isolated from the inflamed synovium of mice with AIA, and from mice before the induction of AIA (taken as control tissues). ATAC-seq was performed using 100,000 nuclei per sample as described in the manufacturer's instruction protocol (Illumina, FC-121-1030). After amplification, library DNA was isolated (Qiagen MiniElute kit), size selected, and sequenced (Illumina HiSeq4000). All samples were quantified (Qubit; Invitrogen) before sequencing (Illumina HiSeq4000; 40-70M reads/sample). ATAC-seq libraries were generated from fresh cells using the ATAC-Seq Kit (Active Motif, catalog# 53150). Libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and profiled using the D5000 ScreenTape on TapeStation 4200 (Agilent Technologies).