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Access GEO data and retrieve fastQ files

Hi everyone,

I am interested in data about mouse pancreatic tumor that are available at this adress : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4293554

I have found the sra-toolkit package that gives functions to extract fastQ files from SRR, that works fine. However, I have these questions about it :

Is there a reason why there are plenty of SRR files for a unique sample? I haven't read something justifying it - according to authors description, they dissociated the pancreas and then send it to sequencing Don't we get only multiple runs according to sequencer lanes? I guess I should just download all the SRR by sample and merge the sequences together?

Thank you so much for your time,

Wish you a great day,

geo fastq
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updated by Ram Ram • written by Hojn • Hojn

1 answer

Looking at the experimental design it says this:

Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice at six different time points post-tamoxifen injection (PTI)

So there are at least 36 (or even more) samples included in this submission. You will probably need to check the associated publication to see which SRR* accessions relate to which samples.

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written by GenoMax GenoMax

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