Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN12582139, SRS5276899

collection date

2013-08-12

derived-from

This BioSample is a metagenomic assembly obtained from the termite gut metagenome BioSample: SAMN03344614

env_broad_scale

woodland biome

env_local_scale

tropical woodland biome

env_medium

digestive tract

environmental sample

1

geo loc name

Republic of the Congo: Pointe-Noire

host

Termes hospes

host body habitat

gut

host diet

Humus feeder

isolate

Th196P3_bin2

isolation source

P3 gut compartment

lat lon

4.42 S 11.4949 E

metagenome source

termite gut metagenome

metagenomic

1

sample-type

metagenomic assembly

type-material

reference material of Candidatus Methanoplasma cognatum

Termes hospes P3

BioSample Accession(s)

SAMN03344614

collection date

2013

geo loc name

Democratic Republic of the Congo

host

Termes hospes

isolation source

P3

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX6724923" alias="Th196P3_bin2" center_name="SUB6185198" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX6724923</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB6185198">Th196P3_bin2</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Binning of metagenomic reads from  the P3 gut compartment of Termes hospes</TITLE>
  <STUDY_REF accession="SRP218535">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP218535</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA560329</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Genome reconstructed from a termite gut metagenome suing MetaBAT2.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS5276899">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS5276899</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN12582139</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Th196P3_bin2</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS5276899</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA942061</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=SRX6724923&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=SRX6724923&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX952256" alias="Th196P3 iTAG" center_name="Max Planck Institute for Terrestrial Microbiology" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX952256</PRIMARY_ID>
    <SUBMITTER_ID namespace="Max Planck Institute for Terrestrial Microbiology">Th196P3 iTAG</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Th196P3 termite gut iTAG</TITLE>
  <STUDY_REF accession="SRP116658">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP116658</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA280402</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS872428">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS872428</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03344614</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME/>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_SDEV="0.0E0"/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>300</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>151</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS872428</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA246311</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=SRX952256&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=SRX952256&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>