Deducing AIRR-seq Library Generation From SRA Data

Question

[A Soggy Waffle]

I'm trying to run airrflow on some data from the SRA. My problem is my airrflow runs die immediately, complaining that I must supply the library_generation_method parameter and I can't find that info attached to this data anywhere. The "library" value in the SRA Run Selector for this experiment isn't helpful either. Maybe this stuff is common knowledge in the immunology community and I'm out of the loop.

Without finding an a publication for the associated study, I assume I should use specific_pcr for that parameter. However, that requires also specifying the primers used. My next move is googling until I find all B cell isotypes and what nucleotides make their CH7 domain, and generating my own primers from that.

BUT, my initial assumption could be wrong. So I ask you all, is such assumption reasonable? Is it possible to figure out what library generation was used? Is there an easier/faster way to get these primers?

Thank you

[GenoMax]

Experiment page for this submission --> https://www.ncbi.nlm.nih.gov/sra/SRX9255352

has the following description

Total RNA was used to synthesize cDNA, using the Superscript IV First-Strand Synthesis System (Invitrogen), with primers targeting the immunoglobulin heavy chain CH7 domain of each isotype according to the manufacturers protocol. SPRI beads (AmpureXP, Be

[A Soggy Waffle]

Thanks for the reply. However, I already looked at all the associated data with ( experiment, bioproject, biosample ) and did not find the answer I'm looking for. I bolded the parts of the original post that I'm really trying to get help for.

[GenoMax]

You could try writing to the submitter and ask for that information? Simply googling may not give you exact info.

[A Soggy Waffle]

EDIT: I found the submitter buried in the related BioSample submissions. All other places just say "Seoul National University".

Thank you for your time and input. I appreciate that you tried to help answer my questions.

Answer 1

[A Soggy Waffle]

I found useful resources for immunoglobulin sequences and primers. Putting them here if some future traveler stumbles onto this post.

Also, I figure this is as far as this post needs to go so I'll mark this as the "answer".

IMGT Reference Sequence DB

IMGT Primer DB