BioSample Accession(s)

SAMN03859889

collection date

2014-01-01

environmental sample

true

geo loc name

USA: San Diego

host

Homo sapiens

isolate

12B

isolation source

oral subgingival plaque

metagenome source

human oral metagenome

metagenomic

true

sample type

metagenomic assembly

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1288281" alias="Periodontal Metagenome 12B" center_name="University of Washignton" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1288281</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Washignton">Periodontal Metagenome 12B</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Periodontal Metagenome Study (SDSU) Sample 12B</TITLE>
  <STUDY_REF accession="SRP064209">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP064209</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA289925</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Paired-End Illumina Metagenome</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS1090535">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS1090535</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03859889</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>12B_perio</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>unspecified</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="100" NOMINAL_SDEV="0.0E0"/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>200</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Forward</READ_TYPE>
          <BASE_COORD>1</BASE_COORD>
        </READ_SPEC>
        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>101</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS1090535</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA301051</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=SRX1288281&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=SRX1288281&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</TAG>
      <VALUE>PUBLIC</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>