NCBI SRA database sample: control vs test

Question

[dpc]

I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But I am unable to understand which samples are 'control' and 'test' samples. Please help me regarding how to differentiate the samples.

[GenoMax]

Is there an associated publication? You may need to check that.

[ATpoint]

Hello DEEP!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/11678/ncbi-sra-database-sample-control-vs-test

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Istvan Albert]

Unfortunately, that information seems not specified, at least I was unable to locate after searching for it. You can see the runinfo CSV file like so:

esearch -db sra -query PRJNA177201 | efetch -format runinfo > out.csv

or the following gives you an even more detailed XML:

esearch -db sra -query PRJNA177201 | efetch -format xml > out.xml

Yet neither contains the most important information, which one is the control and what is the tested condition. The most I found is that samples are named like so:

Symptomatic atherosclerosis gut metagenome 150

see if you could connect the number 150 to a sample type after reading the paper and supplementary information.

Also, an option is to write the authors for the information.

[dpc]

Thanks Istvan for your suggestion...