As part of the RR-12 mission, we vaccinated female C57BL6 mice with the tetanus toxoid with or without CpG adjuvant. We have CDR3 data for both T and B cells after either one our two exposures to the vaccine, generated by iRepertoire (https://irepertoire.com/).
There were two experiments on RR-12. The first involved a primary vaccination, where naïve mice were vaccinated after about 2 weeks in orbit and we collected samples 2 weeks later. The second experiment involved mice that were vaccinated on the ground, allowed to develop memory, and then sent to the ISS. Then, after about 2 weeks in orbit, they were vaccinated a second time and tissues were collected two weeks later.
We’ve been struggling with the analysis for three reasons. 1) Because of the way repertoires work and the size of the tetanus toxoid, the response to the vaccine is unique to every mouse, making the analysis extra problematic. 2) The original post doc that was working on the project moved on to industry and we’ve been struggling to find a replacement with the necessary expertise. And 3) We discovered a bit of contamination in the samples. iRepertoire says that it can be statistically removed, but we’re not sure how to do that yet.
I have been trying to get the IMDA pipeline working (Installation — IMDA 1.0 documentation) but i keep running into roadblocks. It’s a few years old, so there may be a newer better pipeline, but this one seems to do all the things I want to start with once I get it working.
I have a student working on this once he finishes with his classwork, but he’s starting from ground zero and had to learn both RNAseq and antibody VDJ recombination before he could even begin to work on this.
Any help on this would be appreciated.