GSM7846355: ATAC-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep3); Mus musculus; ATAC-seq
Mice were anaesthetized with isoflurane (adjusted flow rate or concentration to 1.5%) and 50 µl of cardiotoxin (10x10-6 M in PBS) (Latoxan) was injected in the tibialis anterior (TA) muscle. Muscles were recovered for flow cytometry analysis at day 1,2 and 4 post-injury and were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cint F4/80- neutrophils were quantified and sorted. For ATAC-seq experiment, ATAC-seq lysis buffer was added, followed by DNA tagmentation according to Buenrostro  et al (PMID: 25559105). Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.