Search SRA metadata for Histological_Type and Body_Site

Question

[oakhamwolf]

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.

Cheers

Answer 1

[GenoMax]

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)
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
SRR23348218,2023-05-01 00:08:01,2023-02-06 11:18:42,1364164,207352928,1364164,152,82,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR023/23348/SRR23348218/SRR23348218.lite.1,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 https://sra-explorer.info/ and search with terms you want to get URL's for download.