*4.5. RNA Sequencing and Data Analysis*

*C57Bl*/*6J* injured and uninjured joints from VEH-, AB-, and LPS-treated male and female mice were collected 24 h after injury (*n* >= 4). Joints were dissected and cut at the edges of the joint region with small traces of soft tissue to preserve the articular integrity. RNA was isolated and sequenced as previously described [36]. RNA-seq data quality was checked using FastQC software (version 0.11.5). Sequence reads were aligned to the mouse reference genome (mm10) using STAR (version 2.6). After read mapping, 'featureCounts' from Rsubread package (version 1.30.5) was used to perform read summarization to generate gene-wise read counts. Differentially expressed genes (DEGs) were identified using edgeR (version 3.22.3). Genes with a false discovery rate (FDR) corrected *p*-value less than 0.05 and fold change greater than 1.5 were considered as DEGs. Heatmaps were generated using heatmap.2 function in R package 'gplots'.
