Question: fetch all relevant datasedts from GEO database
gravatar for APJ
4 weeks ago by
APJ20 wrote:


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?

eutils ncbi geo • 83 views
ADD COMMENTlink written 4 weeks ago by APJ20

What have you tried?

ADD REPLYlink written 4 weeks ago by Kevin Blighe51k

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

ADD REPLYlink written 4 weeks ago by APJ20

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.

ADD REPLYlink written 4 weeks ago by ATpoint25k

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!

ADD REPLYlink written 4 weeks ago by APJ20
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