collection_date

2011-07-12

note

This biosample is a metagenomic assembly obtained from the subsurface metagenome BioSample: SAMN03166137

type-material

reference material of Candidatus Hydrothermus pacificus

organism

Candidatus Hydrothermus pacificus

metagenomic

TRUE

sample_type

metagenomic assembly

environmental-sample

TRUE

metagenome-source

subsurface metagenome

isolate

JdFR-72

NCBI submission package

Microbe.1.0

depth

454

publication

Jungbluth_etal_ScientificData

geo_loc_name

Pacific Ocean

env_biome

hydrothermal fluid

lat_lon

47.76 N 127.76 W

isolation_source

basaltic crustal fluids

BioSampleModel

Microbe, viral or environmental

ENA-FIRST-PUBLIC

2017-01-17

ENA-LAST-UPDATE

2024-06-23

SSU rRNA gene survey of Hole U1362A basaltic crustal fluids

collection_date

2011-07-12

misc_param

Subsurface_Fluids_21-22_U1362A

env_feature

borehole

INSDC secondary accession

SRS738698

organism

subsurface metagenome

GOLD Ecosystem Classification

Environmental | Aquatic | Marine | Hydrothermal vents | Diffuse flow

NCBI submission package

MIMARKS.survey.sediment.6.0

depth

454

env_material

water

elev

-2667

geo_loc_name

Pacific Ocean

env_biome

hydrothermal fluid

lat_lon

47.76 N 127.76 W

BioSampleModel

MIGS/MIMS/MIMARKS.sediment

ENA-FIRST-PUBLIC

2014-11-06

ENA-LAST-UPDATE

2022-10-21

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1880758" alias="JGI-SRA-8752" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1880758</PRIMARY_ID>
    <EXTERNAL_ID namespace="JGI">JGI-SRA-8752</EXTERNAL_ID>
  </IDENTIFIERS>
  <TITLE>Deep oceanic, basalt-hosted subsurface fluids, CORK Borehole 1362A_J2.573</TITLE>
  <STUDY_REF accession="SRP049601">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP049601</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA266365</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS738698">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS738698</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03166137</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>UCHB</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Regular (DNA)</LIBRARY_CONSTRUCTION_PROTOCOL>
    </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>SRS738698</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA436150</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=SRX1880758&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=SRX1880758&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>