fetch all relevant datasedts from GEO database
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3.1 years ago
APJ ▴ 40

Hi,

I would like to retrieve relevant studies available on GEO database for my search terms.

For example: I am interested in RNA-seq datasets published for a particular gene X which has a role in kidney disease. The experimental design should include control and study group with minimum of10 replicate samples.

How do I fetch relevant GEOseries using ncbi-eutils? Any ideas please?

GEO NCBI eutils • 547 views
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What have you tried?

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I tried the hard way through the GEO DataSets Advanced Search Builder, which takes multiple query terms to fetch the results.

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By best knowledge there is no ready-to-use approach that is that specific and frees you from the unpleasant manual search. You will have to do it the old-fashioned way, using PubMed, google and tools like sra-explorer plus a lot of individual effort.

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Yes, I was doing the manual search. But interested to know, if there is any easy and better way of searching. Thanks for sra-explorer link!

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