fetch all relevant datasedts from GEO database

0

Entering edit mode

4.5 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 • 772 views

ADD COMMENT • link 4.5 years ago by APJ ▴ 40

1

Entering edit mode

What have you tried?

ADD REPLY • link 4.5 years ago by Kevin Blighe 87k

0

Entering edit mode

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

ADD REPLY • link 4.5 years ago by APJ ▴ 40

0

Entering edit mode

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 REPLY • link 4.5 years ago by ATpoint 81k

0

Entering edit mode

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 REPLY • link 4.5 years ago by APJ ▴ 40

Login before adding your answer.