RNA-Seq quantification and differential expression analysis

RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic⁵¹. Sequence alignment was performed using STAR⁵² against the Human genome (GRCH.38; GCF_000001405.38) with the default parameters. The expression of each gene was quantified using HTSeq⁵³. Differential gene expression analysis was accomplished using DESeq2. After Benjamini-Hochberg FDR correction, genes with adjusted p-values less than 0.05 and fold change greater than 1.5 were considered as differentially expressed genes (DEGs). Raw data is deposited at the Gene Expression Omnibus and Short Read Archive (accession numbers: {"type":"entrez-geo","attrs":{"text":"GSE145789","term_id":"145789"}}GSE145789). Functional annotation and gene set enrichment analysis of the top 200 differentially expressed genes was carried out using Metascape (http://metascape.org/).