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UseGalaxy.eu Use Case: Antibody responses following vaccination

Carolyn Nielsen works on clinical immunology at the University of Oxford (UK).

My project focuses on understanding the cellular drivers of antibody responses following vaccination, in particular in the impact of different dosing regimens. As part of this work, I have run a single cell RNA sequencing experiment (SmartSeq, Nextera, HiSeq4000) with sorted vaccine-specific B cells from two groups receiving malaria vaccines on either a ‘standard’ or ‘delayed’ dosing regimen. I am now analysing this data using the Human Cell Atlas of the Galaxy platform to understand whether there is differential gene expression between the B cell responses of the two groups, which would give important insight into the impact of dosing regimen on the quality of the B cell response. As a non-bioinformatician, the Galaxy platform has been invaluable to me as an accessible tool to explore the gene expression data, building analysis skills without needing to devote an extensive period of time to learning to code or use command line programmes. The storage capacity of the platform has also meant that after the initial data upload I can run my analysis anywhere, and without requiring subscription to sequencing facilities/servers. I plan to finish this analysis within the next few months and include in an upcoming publication.

Thank you Carolyn for using Galaxy and sharing your research with us!