Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN41134099, SRS26337081

isolate

S340_Human-SFB-ML-1

collection_date

NA

env_broad_scale

Feces

env_local_scale

NA

env_medium

NA

geo_loc_name

NA

isolation_source

gut

lat_lon

NA

host

Homo sapiens

metagenomic

1

environmental-sample

1

sample_type

metagenomic assembly

metagenome_source

human gut metagenome

derived-from-SRA

SRR35183424, SRR35215812, SRR35215811, SRR35215810

ncbi_package

MIMAG.human-gut.6.0

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30319628" alias="SL325472" center_name="SUB15585069" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30319628</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15585069">SL325472</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>RNA baits capture of Mali 340</TITLE>
  <STUDY_REF accession="SRP614497">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP614497</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1106451</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>S340 illumina sequences (BAIT captured 1x)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26337081">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26337081</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN41134099</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SL325472</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGA</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26337081</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2210890</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319628&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319628&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30319627" alias="HiC_Malien340" center_name="SUB15585069" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30319627</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15585069">HiC_Malien340</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>HiC of Mali 340</TITLE>
  <STUDY_REF accession="SRP614497">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP614497</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1106451</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>S340 illumina sequences (HiC)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26337081">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26337081</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN41134099</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>HiC_Malien340</LIBRARY_NAME>
      <LIBRARY_STRATEGY>Hi-C</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26337081</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2210890</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319627&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319627&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30319629" alias="340_IP" center_name="SUB15585069" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30319629</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15585069">340_IP</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>RNA baits capture of Mali 340</TITLE>
  <STUDY_REF accession="SRP614497">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP614497</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1106451</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>S340 pacbio sequences (BAIT captured 1x)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26337081">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26337081</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN41134099</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>340_IP</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGA</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <PACBIO_SMRT>
      <INSTRUMENT_MODEL>PacBio RS</INSTRUMENT_MODEL>
    </PACBIO_SMRT>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26337081</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2210890</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319629&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30319629&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30288300" alias="S8" center_name="SUB15534396" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30288300</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15534396">S8</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>WGS of Mali 340: fecal DNA</TITLE>
  <STUDY_REF accession="SRP614497">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP614497</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1106451</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>S340 illumina sequences</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26337081">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26337081</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN41134099</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>S8</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26337081</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2208454</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30288300&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30288300&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX30618522" alias="Mali_S340_2_16S" center_name="SUB15656606" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX30618522</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15656606">Mali_S340_2_16S</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PacBio 16S rRNA gene sequencing data</TITLE>
  <STUDY_REF accession="SRP614497">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP614497</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1106451</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Mali S340 PCR amplification of the full-length 16S rRNA</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS26337081">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS26337081</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN41134099</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Mali_S340_2_16S</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <PACBIO_SMRT>
      <INSTRUMENT_MODEL>PacBio RS II</INSTRUMENT_MODEL>
    </PACBIO_SMRT>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS26337081</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2230026</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30618522&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRX30618522&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>