Question: RNA Seq version of GEO data sets?
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gravatar for StephanieK
2.6 years ago by
StephanieK90
StephanieK90 wrote:

Hi all, I downloaded a set of mammalian ageing-related gene expression data sets (GDS files) from GEO using the filter:

(("age"[Subset Variable Type]) OR "development stage" [Subset Variable Type]) AND "mammals" [Organism]

Now, I want to download all of the RNA seq data sets for mammalian ageing-related gene expression data sets.

From what I understand, for RNASeq, I can't download the gene expression data sets (GDS files in GEO), I have to download the raw SRA reads (which I presume are like .CEL files), read them in to some software, and obtain the gene expression values myself?

So in the NCBI SRA database, I tried to use this filter:

(("age"[Subset Variable Type]) OR "development stage" [Subset Variable Type]) AND "mammals" [Organism] AND gds_sra[filter]

But I got no results.

I've also seen some other databases, such as ArrayExpress. What I'm wondering (1) Does NCBI SRA database have the data I am looking for and (2) Why does my command to filter and retrieve the set of mammalian ageing-related data sets not work? I assumed that NCBI would have the most comprehensive collection of data, hence why I am focusing on trying to extract data from there.

Thanks

rna-seq gene expression geo • 819 views
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