Keywords: GSC:MIxS;MIGS:6.0

BioSample Accession(s)

SAMN36439001, SRS19697985

extrachrom_elements

1

strain

PD1

collection_date

2016-07-02

isol_growth_condt

N/A

ref_biomaterial

N/A

temp

85 C

INSDC secondary accession

SRS19697985

rel_to_oxygen

microaerophilic

organism

Candidatus Fervidibacter sacchari

biotic_relationship

free living

env_broad_scale

hot spring [ENVO:00000051]|

env_local_scale

sediment [ENVO:00002007]

NCBI submission package

MIGS.ba.sediment.6.0

depth

0

elev

1208 m

num_replicons

2

geo_loc_name

USA: Great Boiling Spring, Gerlach, NV

env_medium

sediment [ENVO:00002007]

lat_lon

40.661472 N 119.366139 W

isolation_source

hot spring sediment

BioSampleModel

MIGS/MIMS/MIMARKS.sediment

ENA-FIRST-PUBLIC

2023-07-13

ENA-LAST-UPDATE

2023-12-01

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX22705682" alias="Nanopore library" center_name="SUB14011852" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX22705682</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB14011852">Nanopore library</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Long-read genomic sequencing of Fervidibacter sacchari PD1</TITLE>
  <STUDY_REF accession="SRP475307">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP475307</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA994580</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Sequencing library prepared with the Native Barcoding Expansion (EXP-NBD104) and Ligation Sequencing (SQK-LSK109) kits using Nanopore protocol version NBE_9065_v109_revAH_14Aug2019 and sequenced on an Oxford Nanopore MinION Mk1B device using a FLO-MIN106 flow cell.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS19697985">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS19697985</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN36439001</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Nanopore library</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>SRS19697985</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1761080</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=SRX22705682&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=SRX22705682&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX22705681" alias="Illumina library" center_name="SUB14011852" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX22705681</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB14011852">Illumina library</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Short-read genomic sequencing of Fervidibacter sacchari PD1</TITLE>
  <STUDY_REF accession="SRP475307">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP475307</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA994580</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Paired-end 2x150 bp configuration</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS19697985">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS19697985</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN36439001</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Illumina library</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>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS19697985</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1761080</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=SRX22705681&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=SRX22705681&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>