collection_date

2009-11-08

isolate

CG1_02_44_16

note

This biosample is a metagenomic assembly obtained from the metagenome sample SAMN02419149

NCBI submission package

Metagenome.environmental.1.0

organism

Candidatus Omnitrophica bacterium CG1_02_44_16

metagenomic

TRUE

geo_loc_name

USA: Crystal Geyser near Green River, Utah

lat_lon

38.56 N 110.8 W

environmental-sample

TRUE

isolation_source

groundwater filtered through a a 3.0 um filter and then through a 0.2 um filter

metagenome-source

groundwater metagenome

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2016-02-23

ENA-LAST-UPDATE

2021-02-28

Keywords: GSC:MIxS;MIMS:5.0

collection_date

2009-11-08

temp

17

INSDC secondary accession

SRS672319

rel_to_oxygen

microaerophilic

organism

groundwater metagenome

project_name

Crystal Geyser metagenome

NCBI submission package

MIMS.me.miscellaneous.5.0

feature

geyser

material

water

biome

subsurface

geo_loc_name

USA: Crystal Geyser near Green River, Utah

investigation_type

metagenome

env_package

MIGS/MIMS/MIMARKS.miscellaneous

lat_lon

38.56 N 110.8 W

isolation_source

groundwater filtered through a a 3.0 um filter and then through a 0.2 um filter

BioSampleModel

MIGS/MIMS/MIMARKS.miscellaneous

ENA-FIRST-PUBLIC

2013-11-22

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX667739" alias="CrystalGeyser_CG2_0.2B" center_name="University of California, Berkeley" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX667739</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of California, Berkeley">CrystalGeyser_CG2_0.2B</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Crystal Geyser Metagenome CG2 sample 0.2 micron filter B</TITLE>
  <STUDY_REF accession="SRP045164">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP045164</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA229517</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Single samples from a 0.2 micron filter</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS672319">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS672319</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN02419149</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>CG2_0.2B</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>padlock probes capture method</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="200" NOMINAL_SDEV="20"/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>200</SPOT_LENGTH>
        <READ_SPEC>
          <READ_INDEX>0</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Forward</READ_TYPE>
          <BASE_COORD>1</BASE_COORD>
        </READ_SPEC>
        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>101</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <PROCESSING/>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS672319</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA177547</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=SRX667739&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=SRX667739&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>