Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN46472259,

isolate

FB10N2-isolate

isolation_source

intertidal mud flat

collection_date

2015-06-03

geo_loc_name

USA: WA, San Juan Is, False Bay

lat_lon

48.4855 N 123.0753 W

sample_type

metagenomic assembly

depth

missing

elev

missing

env_broad_scale

missing

env_local_scale

missing

env_medium

missing

metagenomic

1

environmental-sample

1

metagenome_source

sediment metagenome

derived_from

SAMN40276086

ncbi_package

MIMAG.sediment.6.0

BioSample Accession(s)

SAMN40276086, SRS20691575

collection_date

2015-06-03

rel_to_oxygen

anaerobe

ENA-FIRST-PUBLIC

2025-03-21

organism

sediment metagenome

ENA-LAST-UPDATE

2025-03-21

BioSampleModel

Metagenome or environmental

geo_loc_name

USA: WA, San Juan Is, False Bay

scientific_name

sediment metagenome

lat_lon

48.4855 N 123.0753 W

isolation_source

intertidal mud flat

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27466925" alias="FB10N2_barcode63" center_name="SUB15027554" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27466925</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15027554">FB10N2_barcode63</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw metagenomic sequencing reads for FB10N2</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1084235</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was extracted from duplicate cultures grown for seven days in 3% LB-SW (45 ml) at room temperature under microaerophilic conditions. The DNA was treated with 1 mg/ml RNase A, quantified with the Qubit dsDNA HS assay kit, and stored at -20C.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691575">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691575</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276086</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>FB10N2_barcode63</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>size fractionation</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691575</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2060292</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=SRX27466925&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=SRX27466925&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="SRX27521217" alias="FB10N2_lib609350_10076_3" center_name="SUB15049977" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27521217</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15049977">FB10N2_lib609350_10076_3</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>FB10N2_1</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1084235</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Paired-end sequencing of breviate-associated bacterial communities, processed using Eurofins' INVIEW Metagenome pipeline</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691575">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691575</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276086</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>FB10N2_lib609350_10076_3</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691575</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2065010</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=SRX27521217&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=SRX27521217&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="SRX27521218" alias="FB10N2_lib609350_8172_1" center_name="SUB15049977" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27521218</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15049977">FB10N2_lib609350_8172_1</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>FB10N2_2</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1084235</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Paired-end sequencing of breviate-associated bacterial communities, processed using Eurofins' INVIEW Metagenome pipeline</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691575">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691575</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276086</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>FB10N2_lib609350_8172_1</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691575</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2065010</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=SRX27521218&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=SRX27521218&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>