BioSample Accession(s)

SAMN00102804

Funding Program

DOE-CSP 2010

GOLD Stamp ID

Gi06207

Gene Calling Method

Prodigal 1.4, GenePRIMP

Gram Staining

Gram-

Isolation Comments

isolated by M Svenning

Sporulation

Nonsporulating

Type Strain

Yes

biotic relationship

free living

cell shape

Rod-shaped

collection date

1996

country

Svalbard

culture-collection

DSM:17260

environment

Soil

investigation type

bacteria_archaea

isol_growth_condt

16403874

isolation site

Artic wetland soil

isolation-source

arctic wetland soil

lat lon

78.924 N 11.955 E

motility

Nonmotile

num_replicons

1

project name

Methylobacter tundripaludum SV96

ref_biomaterial

DSM 17260, ATCC BAA-1195

rel_to_oxygen

aerobe

strain

SV96

temperature optimum

23C

temperature range

Mesophile

trophic_level

methylotroph

type material

type strain of Methylobacter tundripaludum

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1953011" alias="JGI-SRA-20166" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1953011</PRIMARY_ID>
    <EXTERNAL_ID namespace="JGI">JGI-SRA-20166</EXTERNAL_ID>
  </IDENTIFIERS>
  <TITLE>Methylobacter tundripaludum SV96</TITLE>
  <STUDY_REF accession="SRP002716">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP002716</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA48297</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS107395">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS107395</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN00102804</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>GUHU</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Solexa paired ends</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina Genome Analyzer II</INSTRUMENT_MODEL>
    </ILLUMINA>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
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  <IDENTIFIERS>
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    <SUBMITTER_ID namespace="JGI">GSXWa</SUBMITTER_ID>
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  <TITLE>454 sequencing of Methylobacter tundripaludum SV96 random whole genome shotgun library.</TITLE>
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  <DESIGN>
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      <IDENTIFIERS>
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        <SUBMITTER_ID namespace="JGI">4088565</SUBMITTER_ID>
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    <LIBRARY_DESCRIPTOR>
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      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
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        <READ_SPEC>
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          <BASE_COORD>5</BASE_COORD>
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      </SPOT_DECODE_SPEC>
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  <PLATFORM>
    <LS454>
      <INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL>
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  <PROCESSING/>
  <EXPERIMENT_LINKS>
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  <EXPERIMENT_ATTRIBUTES>
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Metadata as EBI XML

<EXPERIMENT_SET>
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    <SUBMITTER_ID namespace="JGI">HAAUa</SUBMITTER_ID>
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  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>           none provided         </DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS107395" refname="4088565">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS107395</PRIMARY_ID>
        <SUBMITTER_ID namespace="JGI">4088565</SUBMITTER_ID>
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    <SPOT_DESCRIPTOR>
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        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
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          <READ_TYPE>Forward</READ_TYPE>
          <BASE_COORD>5</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
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  <PLATFORM>
    <LS454>
      <INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL>
    </LS454>
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  <PROCESSING/>
  <EXPERIMENT_LINKS>
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      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
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    <EXPERIMENT_LINK>
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  <EXPERIMENT_ATTRIBUTES>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX025748" alias="GTAAa" center_name="JGI" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX025748</PRIMARY_ID>
    <SUBMITTER_ID namespace="JGI">GTAAa</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>454 sequencing of Methylobacter tundripaludum SV96 random whole genome shotgun library.</TITLE>
  <STUDY_REF accession="SRP002716" refname="192">
    <IDENTIFIERS>
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      <SUBMITTER_ID namespace="JGI">192</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>           none provided         </DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS107395" refname="4088565">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS107395</PRIMARY_ID>
        <SUBMITTER_ID namespace="JGI">4088565</SUBMITTER_ID>
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    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>GTAA</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
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    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
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          <READ_INDEX>0</READ_INDEX>
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        <READ_SPEC>
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      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
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  <PLATFORM>
    <LS454>
      <INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL>
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  <PROCESSING/>
  <EXPERIMENT_LINKS>
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      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
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        <DB>ENA-FASTQ-FILES</DB>
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  <EXPERIMENT_ATTRIBUTES>
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</EXPERIMENT_SET>