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Link sample IDs to GEO_Accession ID for analysis of differential expression

Hi there,

I wish to run analysis of counts from a published RNAseq experiment to look for genes that are differentially expressed in a knockdown/knockout cell line, with the aim to identify common transcripts between these data and data produced from my lab. However, I'm unable to match the sample IDs (control/Knockdown) with that of the GEO Accession IDs/SRA runs as the column headers for each run are listed rather ambiguously (e.g. v11, v12, v13 etc.). The dataset I'm looking at is listed here:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124407 GSE124407_RNAseq_count_all_matrix_siRNA.txt.gz
GEO Accessions: GSM3532120-25

I'm able to run the analysis no problem with DESeq and get the genes I need but at the moment its a bit of an educated guess as to which samples the GEOs represent, as I know that the knockout will amplify expression of a gene it normally represses. As such, I'd be grateful for any help or advice on to how to get around this?

Thanks in advance!

rnaseq geo deseq
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updated by GenoMax GenoMax • written by sci_djw • sci_djw

The sample ID's are associated with sample names. They kind of seem explanatory. Is that not the case?

GSM3532120  AsPC1_siBACH1_RNAseq_rep1
GSM3532121  AsPC1_siBACH1_RNAseq_rep2
GSM3532122  AsPC1_siBACH1_RNAseq_rep3
GSM3532123  AsPC1_siCont_RNAseq_rep1
GSM3532124  AsPC1_siCont_RNAseq_rep2
GSM3532125  AsPC1_siCont_RNAseq_rep3
GSM4223708  AsPC1_sgBACH1_rep1
GSM4223709  AsPC1_sgBACH1_rep2
GSM4223710  AsPC1_sgBACH1_rep3
GSM4223711  AsPC1_sgCont_rep1
GSM4223712  AsPC1_sgCont_rep2
GSM4223713  AsPC1_sgCont_rep3
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written by GenoMax GenoMax

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