collection_date

2013-06-03

note

This biosample is a genome obtained from the metagenome sample SAMN03842440

NCBI submission package

Metagenome.environmental.1.0

organism

Omnitrophica bacterium RIFCSPLOWO2_12_FULL_44_17

metagenomic

true

geo_loc_name

USA: Rifle, CO

lat_lon

39.5369 N 107.7828 W

environmental-sample

true

isolation_source

Rifle well FP-101 under low O2 conditions; 1.2 micron filter; full assembly

metagenome-source

subsurface metagenome

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2016-02-22

ENA-LAST-UPDATE

2021-02-28

collection_date

2013-06-03

INSDC secondary accession

SRS981366

NCBI submission package

Metagenome.environmental.1.0

organism

groundwater metagenome

geo_loc_name

USA: Rifle, CO

lat_lon

39.5369 N 107.7828 W

isolation_source

Rifle well FP-101 under low O2 conditions; 1.2 micron filter; full assembly

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2015-07-07

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1085359" alias="SRA_RIFCSPLOWO2_12_FULL" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1085359</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of California, Berkeley">SRA_RIFCSPLOWO2_12_FULL</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Rifle well FP-101 under low O2 conditions; 1.2 micron filter; full assembly</TITLE>
  <STUDY_REF accession="SRP060520">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP060520</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA288027</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>adaptor-trimmed raw reads</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS981366">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS981366</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN03842440</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>SRA_RIFCSPLOWO2_12_FULL</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>300</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>151</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>pubmed</DB>
        <ID>28077874</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS981366</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA276186</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=SRX1085359&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=SRX1085359&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>