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.
@mpecaut I think I should know how to handle the analysis… (first time to hear about this service, but seemingly RNAseq-based anyway) but busy now for other tasks. Could we bring it to the next Animal AWG monthly meeting (June 19)?
I could present it, but Sylvain asked that i try this first. it is definitely RNAseq based, but it’s a bit more complicated than typical transcriptomics.
I’m on Linux. There’s only 6 python scripts with some third party software, I have to change some things to get this working, but I want to start with your information.
@cassianyee have you connected with @mpecaut ? There are some T Cell B Cell repertoire data from Rodent Research 12 that perhaps you, Cassian could assist on?
This thread has details, and Mike presented some preliminary data and solutions as the Animal AWG last week w/ @paula6
Hi @mpecaut ! If you need any help with the RNASeq data preprocessing, RNASeq data analysis (genomic alignment, gene
& transcript-level quantification), RNASeq functional analysis (Differential Gene Expression Analysis &
Gene Set Enrichment Analysis), I can bring my skillset to work.
@paula6 - know if this was taken care of yet through the Animal AWG? Alavia I do know that this has been presented and discussed in the Animal AWG, on how to deal with some data artifacts in @mpecaut data. Thanks for offering to help tackle
I was having some issues with iRepertoire getting the original FASTQ files. what i thought was problems with our network conflicting with their sFTP site turned out to be an issue on their end. late last week, i was told that they think they fixed the problem so I’m going to try to re-download the data today and see what happens.