Keywords: GSC:MIxS;MIGS:5.0

BioSample Accession(s)

SAMN15924605

strain

T-2

collection_date

2013-07

isol_growth_condt

25774153

ref_biomaterial

Hedlund BP, Reysenbach AL, Huang L, Ong JC, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H. Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China. Front Microbiol. 2015 Feb 27;6:157. doi: 10.3389/fmicb.2015.00157. PMID: 25774153; PMCID: PMC4343020.

organism

Hydrogenobacter sp. T-2

env_broad_scale

ENVO:01001227

env_local_scale

geothermal spring

NCBI submission package

MIGS.ba.microbial.5.0

depth

0.5 m

elev

1500 m

num_replicons

10

geo_loc_name

China: Rehai Geothermal Field, Tengchong

env_medium

geothermal spring water

lat_lon

24.95093 N 98.43626 E

isolation_source

geothermal spring water

BioSampleModel

MIGS.ba

ENA-FIRST-PUBLIC

2021-09-30

ENA-LAST-UPDATE

2021-09-30

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX29525071" alias="Illumina T-2" center_name="SUB15434856" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX29525071</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15434856">Illumina T-2</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Short-read Illumina sequencing of Hydrogenobacter sp. T-2</TITLE>
  <STUDY_REF accession="SRP598130">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP598130</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA659730</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>0.3 g of wet cell pellet of the T-2 strain was sent for DNA extraction and sequencing at The Sequencing Center (Fort Collins, CO, USA) using the Illumina MiniSeq system with a paired-end 2 x 150 bp configuration. Library preparation was performed with the MiniSeq Reagent kit (FC-420-1003) and Nextera XT Library Preparation kit (FC-131-1096).</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS25657773">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS25657773</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN15924605</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Illumina T-2</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 MiniSeq</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX29525072" alias="Nanopore T-2" center_name="SUB15434856" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX29525072</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15434856">Nanopore T-2</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Long-read Nanopore sequencing of Hydrogenobacter sp. T-2</TITLE>
  <STUDY_REF accession="SRP598130">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP598130</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA659730</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>0.3 g wet cell pellet was used for DNA extraction using a modified version of the JGI bacterial CTAB extraction protocol (https://jgi.doe.gov/user-programs/pmo-overview/protocols-sample-preparation-information/jgi-bacterial-dna-isolation-ctab-protocol-2012/). Modifications to this protocol consisted of three freeze-thaw cycles following the lysozyme treatment, in a dry ice/ethanol bath and a water bath at 65 C for three minutes per cycle, and the use of RNase A (Promega, Madison, WI, USA, catalog number: A7973) for denaturation of ribonucleic acids, and an additional extraction step with chloroform/isoamyl after treatment with RNase A. The sequencing library was prepared with the SQK-LSK109 Ligation Sequencing Kit using the EXP-NBD104 Native Barcoding Expansion Kit (Oxford Nanopore Technologies, Oxford, UK), following the manufacturers instructions and sequenced with a MinION Mk1B device (Oxford Nanopore Technologies, Oxford, UK) with a FLO-MIN106D flow cell.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS25657773">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS25657773</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN15924605</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Nanopore T-2</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>SRS25657773</ID>
      </XREF_LINK>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2163347</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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