control and test samples name of PRJEB12123

Hi there!!! I want to analyse already submitted nucleotide sequence data in European Nucleotide Archive (ENA) with project number PRJEB12123. There are total 257 runs. But I am struggling to understand which runs are of control and which are from test samples. I have read the article and the supplementary informations but failed to understand. I've also contacted the author but no reply. Can anyone of you help me?

Thanks and Regards, DC7

click here for the article

click here to go PRJEB12123

sequencing sra metagenomics

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written 6.2 years ago by dpc

Seems like metadata is provided only in BioSample, you will need to extract all that, for ENA you can get the XML as https://www.ebi.ac.uk/ena/data/view/ERS1015612&display=xml&download=xml&filename=ERS1015612.xml

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written 6.2 years ago by JC

Metadata submitted for these samples don't seem to include this information so you may need to check on the supplementary materials again.

$ esearch -db sra -query "PRJEB12123" | elink -target biosample | efetch -format runinfo | head -30
1: SZAXPI022008-94
Identifiers: BioSample: SAMEA3708714; SRA: ERS1015863
Organism: human gut metagenome
Attributes:
    /Alias="SZAXPI022008-94"
    /ENA checklist="ERC000015"
    /INSDC center name="BGI"
    /INSDC first public="2016-05-31T17:01:44Z"
    /INSDC last update="2016-10-21T09:37:04Z"
    /INSDC status="public"
    /SRA accession="ERS1015863"
    /sample name="ERS1015863"
    /Title="Stool sample from China"
    /collection date="2014"
    /broad-scale environmental context="human gut"
    /local-scale environmental context="human-associated habitat"
    /environmental medium="faeces"
    /geographic location="China"
    /geographic location="China"
    /geographic location (latitude)="55.676097"
    /geographic location (longitude)="12.568337"
    /human gut environmental package="human-gut"
    /investigation type="metagenome"
    /project name="MetaHIT-IGC"
    /sequencing method="Illumina"
Accession: SAMEA3708714 ID: 5194228

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written 6.2 years ago by GenoMax

Yes!!! Nowhere the information has been mentioned. Also authors not responding. Bad luck!!!

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written 6.2 years ago by dpc

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