Search SRA metadata for Histological_Type and Body_Site
Entering edit mode
4 months ago
oakhamwolf ▴ 20

Hi all,

I would like to extract some RNA-Seq (short read or long) datasets from SRA that are from a particular tissue. I know you can search and retrieve metadata by searching with the SRA run or project ID using a number of methods that have already been mentioned on this forum (e.g., esearch and efetch etc) and in doing so, among the meta data fields are Histological_Type and Body_Site.

Is there a way of using these fields to obtain SRA runs or projects where the e.g., Body_Site is "Striatum" or "Retina" etc?

Many thanks for any help in advance.


sra • 176 views
Entering edit mode
4 months ago
GenoMax 134k

While that is one of the optional fields in SRA records, very few entries have that field populated. (or so it appears). Your best best may be to do a search this way

$ esearch -db sra -query "retina AND RNAseq" | efetch -format runinfo (including only one record here there are 1756)
SRR23348218,2023-05-01 00:08:01,2023-02-06 11:18:42,1364164,207352928,1364164,152,82,,,SRX19290017,GSM7026888,RNA-Seq,cDNA,TRANSCRIPTOMIC SINGLE CELL,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP421145,PRJNA931936,,931936,SRS16691033,SAMN33138837,simple,10090,Mus musculus,GSM7026888,,,,,,,no,,,,,"NEUROSCIENCE, JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE",SRA1585200,,public,DF29C73FF0B08558B5B82EA0E25F8D09,AE91D02841A3FC8962416440DD5A29CD

Additional option is to use and search with terms you want to get URL's for download.


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