RNA sequencing became a common method to understand the impact of infection, disease states, and vaccination. There are different flavors of RNA sequencing, from the traditional whole transcriptome sequencing to targeted sequencing, such as the immune repertoire sequencing. There is currently limited understanding of B cell receptor (BCR) repertoires and the early transcriptional changes early after vaccination. For that reason, we aim to study these phenomena using both of these RNA sequencing methods in the context of responses to different vaccination platforms and adjuvants. We have samples from macaques that were vaccinated with different vaccine platforms and sequenced across different timepoints and tissues. We have performed for one of the studies bulk RNA-seq, while for other we have done scRNA-seq couple with scVDJ-seq. From these data we aim to capture differences in the immune repertoires and innate immunity gene signatures induced by vaccination and their impact in later adaptive/antibody responses.
In order to analyze the complex data generated, we will use state of the art pipelines, such as nf-core/rnaseq for bulk preprocessing, but also custom R and python programming scripts. Finally, with these data we hope to gain insights into how different vaccines modulate innate and adaptive immune responses.