Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN46472255

collection_date

2016-07

metagenome_source

sediment metagenome

organism

Desulfovibrio sp.

environmental_sample

true

env_broad_scale

missing

metagenomic

true

sample_type

missing

env_local_scale

missing

isolate

PCE-4

NCBI submission package

MIMAG.sediment.6.0

depth

missing

elev

missing

geo_loc_name

Canada: Prince Edward Island

env_medium

missing

lat_lon

46.5000 N 63.4198 W

isolation_source

Lab-grown breviate-bacteria community

sample derived_from

SAMN40276085

BioSampleModel

MIMAG.sediment

ENA-FIRST-PUBLIC

2025-03-15

ENA-LAST-UPDATE

2025-03-15

BioSample Accession(s)

SAMN40276085, SRS20691574

collection_date

2016-07

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

Canada: Prince Edward Island

scientific_name

sediment metagenome

lat_lon

46.5000 N 63.4198 W

isolation_source

subtidal sediment

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27466926" alias="PCE_barcode51" center_name="SUB15027554" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27466926</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15027554">PCE_barcode51</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw metagenomic sequencing reads for PCE</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="SRS20691574">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691574</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276085</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>PCE_barcode51</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>
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      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691574</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>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27521216" alias="PCE_lib609349_8170_3" center_name="SUB15049977" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27521216</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15049977">PCE_lib609349_8170_3</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>PCE</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="SRS20691574">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691574</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276085</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>PCE_lib609349_8170_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>
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  <EXPERIMENT_LINKS>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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        <ID>SRA2065010</ID>
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    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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      </XREF_LINK>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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      </XREF_LINK>
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  </EXPERIMENT_LINKS>
</EXPERIMENT>
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Metadata as EBI XML

<EXPERIMENT_SET>
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  <TITLE>16S rRNA seq: breviate culture (PCE), 1 week incubation, control</TITLE>
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  <DESIGN>
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    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lib680227_8400</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
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Metadata as EBI XML

<EXPERIMENT_SET>
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    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lib680228_8400</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX23872459" alias="lib680237_8400" center_name="SUB14156873" broker_name="NCBI">
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  <TITLE>16S rRNA seq: breviate culture (PCE), 3 days incubation, control</TITLE>
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    <LIBRARY_DESCRIPTOR>
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Metadata as EBI XML

<EXPERIMENT_SET>
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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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Metadata as EBI XML

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