Keywords: GSC:MIxS;MIMAG:6.0

collection_date

2016-02-01

dreived-from

This BioSample is a metagenomic assembly obtained from the termite gut metagenome BioSample: SAMN13139694

INSDC secondary accession

SRS5276863

organism

Endomicrobiia bacterium

env_broad_scale

woodland biome

metagenomic

1

environmental-sample

1

env_local_scale

tropical woodland biome

metagenome-source

termite gut metagenome

isolate

Emb289P3bin85

NCBI submission package

MIMAG.host-associated.6.0

host_diet

Humus feeder

host

Embiratermes neotenicus

geo_loc_name

French Guiana: Petit-Saut

host_body_habitat

gut

env_medium

digestive tract

lat_lon

5.3454 N 53.2463 W

isolation_source

P3 gut compartment

sample-type

metagenomic assembly

BioSampleModel

MIMAG.host-associated

ENA-FIRST-PUBLIC

2019-10-22

ENA-LAST-UPDATE

2023-03-01

collection_date

2016-02-01

INSDC secondary accession

SRS5706511

NCBI submission package

Metagenome.environmental.1.0

organism

termite gut metagenome

host

Embiratermes neotenicus

geo_loc_name

French Guiana: Petit-Saut

lat_lon

5.3454 N 53.2463 W

isolation_source

P3 gut compartment

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2019-10-28

ENA-LAST-UPDATE

2019-12-10

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX6724887" alias="Emb289P3_bin85" center_name="SUB6185198" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX6724887</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB6185198">Emb289P3_bin85</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Binning of metagenomic reads from  the P3 gut compartment of Embiratermes neotenicus</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="SRS5276863">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS5276863</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN12581797</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Emb289P3_bin85</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 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS5276863</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=SRX6724887&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=SRX6724887&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="SRX7201063" alias="Emb289P3" center_name="SUB6582440" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX7201063</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB6582440">Emb289P3</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Metagenome of Embiratermes neotenicus P3 gut compartment</TITLE>
  <STUDY_REF accession="SRP231247">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP231247</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA590611</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Processing of the termite samples and DNA extraction and purification were described in Rossmassler et al., 2015, Microbiome. Metagenomic libraries were prepared, sequenced, quality controlled, and assembled at the Joint Genome Institute (Walnut Creek, CA, USA).</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS5706511">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS5706511</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN13139694</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Emb289P3</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 2500</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS5706511</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1000572</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=SRX7201063&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=SRX7201063&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>