• Read quality of all the FASTQ files was assessed using FastQC.
• Reads were trimmed using Cutadapt.
• Quality of surviving reads were assessed again using FastQC.
• Results of read quality were summarized using MultiQC.
• High-quality reads were pseudoaligned to the whole human transcriptome (ver. GRCh38.p7) and abundance was quantified using Kallisto.
• Principal component analysis was performed using the R package factoextra.
• Heatmap analysis was performed using the R package pheatmap.
• Differential gene expression analysis was performed using the R/Bioconductor package DESeq.
• Gene set enrichment analysis and overrepresentation analysis were performed using the R/Bioconductor package HTSanalyzeR2.
• Subnetwork analysis was performed using the R/Bioconductor HTSanalyzeR2