Keywords: GSC:MIxS;MIGS:6.0

BioSample Accession(s)

SAMN39855614, ERS18663950

collection_date

1988-01-03

depth

0-2.4 cm

elev

17 m a.s.l.

env_broad_scale

Heathland soil

env_local_scale

Heathland soil with vegetation dominated by Calluna vulgaris (Heather) and Deschampsia flexuosa (Wavy hair-grass)

env_medium

Soil (organic horizon (FH))

geo_loc_name

Netherlands: Hoorneboeg

isol_growth_condt

Minimal medium containing ammonium sulphate as an energy source

lat_lon

52.15 N 5.10 E

num_replicons

3

ref_biomaterial

Primary publication

strain

NHB1

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX34304982" alias="NOB_miseq" center_name="SUB16329714" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX34304982</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB16329714">NOB_miseq</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Miseq sequencing of Ca. Nitrobacter laanbroekii NHB1</TITLE>
  <STUDY_REF accession="SRP717880">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP717880</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1074292</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>A library for paired-end sequencing on the Illumina MiSeq platform was prepared using a Nextera XT kit, according to the manufacturers instructions (Illumina, San Diego, CA, USA)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS29908084">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS29908084</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN39855614</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>NOB_miseq</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS29908084</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2481617</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=SRX34304982&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=SRX34304982&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>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX34304981" alias="NOB_nanopore" center_name="SUB16329714" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX34304981</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB16329714">NOB_nanopore</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Nanopore sequencing of Ca. Nitrobacter laanbroekii NHB1</TITLE>
  <STUDY_REF accession="SRP717880">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP717880</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1074292</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was sheared to approximately 8 kb using a g-TUBE (Covaris, Brighton, UK) and a library prepared with the SQK-MAP006 kit, according to the manufacturers instructions (Oxford Nanopore Technol- ogies, Oxford, UK)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS29908084">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS29908084</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN39855614</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>NOB_nanopore</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>other</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>SRS29908084</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2481617</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=SRX34304981&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=SRX34304981&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>