GSM8443588: Sample_108961; Mus musculus; RNA-Seq
For ATAC-seq, wound macrophages were harvested from mice at day 5 as described above using MACS and nuclei were isolated as described previously (45). For RNA-seq, day 5 wounds were harvested from Setdb2flox/floxLyz2Cre, Stat3flox/floxLyz2Cre, and cre-negative littermate control mice, digested, and underwent negative selection for CD3, CD19, and Ly6G lineage markers. Remaining cells were surface stained and sorted by FACs into CD11b+Ly6CHi and CD11b+Ly6CLo populations. RNA isolation was performed using a RNeasy Kit (Qiagen) with DNase digestion. Library construction and analysis of reads was performed as described previously (41). Briefly, reads were trimmed using Trimmomatic and mapped using HiSAT2 (47, 48). Read counts were performed using the feature-counts option from the subRead package followed by the elimination of low reads, normalization and differential gene expression using edgeR (49, 50). Differential expression was performed on mapped reads using the taqwise dispersion algorithm in edgeR.