BioSample Accession(s)

SAMD00016619

sample comment

This is a metagenomic project to figure out the microbial community flourished along with hot water stream in the Japanese subsurface mine. As a first step of this project, we constructed a fosmid library from the DNA directly isolated from the microbial mat without cultivation. Since we could get about 3,500 fosmid clones, we determined the paired-end sequence of all fosmid clones. We selected putative archaeal genome fragments from the metagenomic library. Total of 132 fosmids were grouped into each 13 or 20 fosmid and each group was analyzed in a half plate of 454 GS20. In addition, 18 fosmids were analyzed by Sanger sequencing. A composite archaeal genome was reconstructed from 91 complete or partial fosmid sequences.

sample name

DRS000201

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="DRX000195" alias="DRX000195" center_name="JAMSTEC" broker_name="DDBJ">
  <IDENTIFIERS>
    <PRIMARY_ID>DRX000195</PRIMARY_ID>
    <SUBMITTER_ID namespace="JAMSTEC">DRX000195</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Sequencing of fosmid clones by 454 GS 20</TITLE>
  <STUDY_REF accession="DRP000160" refcenter="JAMSTEC" refname="DRP000160">
    <IDENTIFIERS>
      <PRIMARY_ID>DRP000160</PRIMARY_ID>
      <EXTERNAL_ID label="BioProject ID" namespace="BioProject">PRJNA39577</EXTERNAL_ID>
      <SUBMITTER_ID namespace="JAMSTEC">DRP000160</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>none provided</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="DRS000201" refcenter="JAMSTEC" refname="DRS000201">
      <IDENTIFIERS>
        <PRIMARY_ID>DRS000201</PRIMARY_ID>
        <EXTERNAL_ID label="BioSample ID" namespace="BioSample">SAMD00016619</EXTERNAL_ID>
        <SUBMITTER_ID namespace="JAMSTEC">DRS000201</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>HGMM Fosmid library</LIBRARY_NAME>
      <LIBRARY_STRATEGY>CLONE</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>none provided</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
        <SPOT_LENGTH>168</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>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <LS454>
      <INSTRUMENT_MODEL>454 GS 20</INSTRUMENT_MODEL>
    </LS454>
  </PLATFORM>
  <PROCESSING>
    <PIPELINE>
      <PIPE_SECTION>
        <STEP_INDEX/>
        <PREV_STEP_INDEX/>
        <PROGRAM>454 Basecaller</PROGRAM>
        <VERSION/>
      </PIPE_SECTION>
    </PIPELINE>
  </PROCESSING>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>DRS000201</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>DRA000160</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=DRX000195&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=DRX000195&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>ENA-STATUS</TAG>
      <VALUE>PUBLIC</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>