bulk RNA-seq of human PBMCs at day 1 after vaccination
The RNA-seq samples were processed using the in-house pipeline. Raw BCL files generated by the sequencer were converted to FASTQ files. CASAVA was used to generate FASTQ files for RNAseq data. Trimmomatic (version 0.33) was used to remove adapters, leading and trailing low-quality bases. Reads less than 36 bases long were dropped. Reads with more than 50% low-quality bases overall were filtered out. The remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (package version 1.2.12); default settings were used for alignment. RSEM uses bowtie2 as aligner to align the mapped reads against the Hg38 reference genome. Data quality control was performed using Picard (version 1.95) and bamtools to obtain general alignment statistics from the bam file.