RNA-Seq data processing and detection of DEGs
The latest version of the human reference genome (GRCh38), gene models, and associated gene annotation information at the time of the study start were obtained from the ENSEMBL database (Version 84, March 2016). The genomic reference was built by merging all human chromosomes except X and Y chromosomes to avoid gender-specific effects. Reads were mapped against the human reference genome using the STAR splice-aware read aligner (Version 2.5.2a) (Genes with expression levels ≤8 CPM for all 50 samples within site were filtered out and were excluded in the differential gene analysis. To identify genes that were significantly differentially expressed (DE) from baseline for each post-vaccination day (Days 1, 2, 7, 14), a negative binomial model was fit to read counts using the implementation provided by the 