Keywords: GSC:MIxS;MIGS:5.0

BioSample Accession(s)

SAMN14057017

strain

T-8

collection_date

2013-07-04

isol_growth_condt

PMID: 25774153

ref_biomaterial

PMID: 25774153

temp

74.6 C

rel_to_oxygen

microaerophilic

organism

Hydrogenobacter sp. T-8

biotic_relationship

free living

env_broad_scale

ENVO:01001227

culture_collection

CGMCC:1.5214

env_local_scale

geothermal spring

NCBI submission package

MIGS.ba.water.5.0

depth

0.5 m

num_replicons

1

ph

6.36

geo_loc_name

China: Rehai Geothermal Field, Tengchong

trophic_level

chemolithoautotroph

env_medium

geothermal spring water

lat_lon

24.95044 N 98.43650 E

BioSampleModel

MIGS.ba

ENA-FIRST-PUBLIC

2020-02-26

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX29674820" alias="T-8 Illumina reads" center_name="SUB15461001" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX29674820</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15461001">T-8 Illumina reads</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Short-read Nanopore sequencing of Hydrogenobacter sp. T-8</TITLE>
  <STUDY_REF accession="SRP600660">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP600660</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA605417</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was isolated using the modified Joint Genome Institute (JGI) CTAB DNA isolation protocol, from a wet cell pellet of ~ 0.5 g obtained by centrifugation of two aliquots of 200 ml culture. The genome was sequenced with Illumina iSeq, with the Nextera DNA Flex Library Prep kit (20018704).</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS25787926">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS25787926</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN14057017</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>T-8 Illumina reads</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina iSeq 100</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS25787926</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2171197</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=SRX29674820&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=SRX29674820&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-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX29674819" alias="T-8 Nanopore reads" center_name="SUB15461001" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX29674819</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15461001">T-8 Nanopore reads</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Long-read Nanopore sequencing of Hydrogenobacter sp. T-8</TITLE>
  <STUDY_REF accession="SRP600660">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP600660</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA605417</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was isolated using the modified Joint Genome Institute (JGI) CTAB DNA isolation protocol, from a wet cell pellet of ~ 0.5 g obtained by centrifugation of two aliquots of 200 ml culture. The genome was sequenced a MinION Mk1B device (Oxford Nanopore Technologies, Oxford, UK) with a FLO-MIN106 flow cell using the SQK-LSK109 Ligation Sequencing Kit and EXP-NBD104 Native Barcoding Expansion Kits.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS25787926">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS25787926</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN14057017</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>T-8 Nanopore reads</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <OXFORD_NANOPORE>
      <INSTRUMENT_MODEL>MinION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS25787926</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2171197</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=SRX29674819&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=SRX29674819&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-ID</TAG>
      <VALUE>4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>