Transcriptome Analysis of Mouse Samples

RNA sequencing libraries were constructed according to the instructions of the manufacturer for the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, China). The libraries were sequenced on the Illumina Nova-seq 6000 platform. The raw sequenced reads were mapped to the mouse genome (mm10) using the STAR software (Dobin et al., 2013 (link)). Genes were annotated using the Ensemble database. The expression of the genes was quantified using HTseq (Anders et al., 2015 (link)), and the differentially expressed genes (DEGs) were identified using DEseq2 (Love et al., 2014 (link)). Genes with FDR < 0.01 and | Log₂ (fold change)| > 1 were considered DEGs. Gene ontology (GO) analysis was performed using the DAVID database (Huang da et al., 2009 (link)). For the ChIRP-seq analysis, raw reads were mapped to the mouse genome (mm10) using the bowtie2 software (Langmead and Salzberg, 2012 (link)). Peaks were called with the MACS suite (Zhang et al., 2008 (link)). Motif enrichment analysis was performed using the MEME suite (Bailey et al., 2015 (link)).