Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN46472268

collection_date

2008-06-06

metagenome_source

sediment metagenome

organism

Pseudodesulfovibrio sp.

environmental_sample

true

env_broad_scale

missing

metagenomic

true

sample_type

missing

env_local_scale

missing

isolate

Pygsuia-isolate-1

NCBI submission package

MIMAG.sediment.6.0

depth

missing

elev

missing

geo_loc_name

USA: MA, Marstons Mills, Prince Cove

env_medium

missing

lat_lon

41.6417 N 70.4134 W

isolation_source

Lab-grown breviate-bacteria community

sample derived_from

SAMN40276089

BioSampleModel

MIMAG.sediment

ENA-FIRST-PUBLIC

2025-03-15

ENA-LAST-UPDATE

2025-03-15

BioSample Accession(s)

SAMN40276089, SRS20691576

collection_date

2008-06-06

rel_to_oxygen

microaerophilic

ENA-FIRST-PUBLIC

2025-03-21

organism

sediment metagenome

ENA-LAST-UPDATE

2025-03-21

BioSampleModel

Metagenome or environmental

geo_loc_name

USA: MA, Marstons Mills, Prince Cove

scientific_name

sediment metagenome

lat_lon

41.6417 N 70.4134 W

isolation_source

soft estuarine sediments

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27466923" alias="Pygsuia_barcode02" center_name="SUB15027554" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27466923</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15027554">Pygsuia_barcode02</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw metagenomic sequencing reads for Pygsuia</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="SRS20691576">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691576</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276089</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Pygsuia_barcode02</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>
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    <EXPERIMENT_LINK>
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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>
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  <TITLE>16S rRNA seq: breviate culture (Pygsuia_biforma), 1 week incubation, anoxic control</TITLE>
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    <LIBRARY_DESCRIPTOR>
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Metadata as EBI XML

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    <LIBRARY_DESCRIPTOR>
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Metadata as EBI XML

<EXPERIMENT_SET>
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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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