Keywords: GSC:MIxS;MIGS:6.0

BioSample Accession(s)

SRS19630906

strain

US3C007

collection_date

2020-09-16

isol_growth_condt

Grown at 22C in AMS1 medium

ref_biomaterial

publication in preparation

INSDC secondary accession

SRS19630906

organism

Alphaproteobacteria bacterium US3C007

env_broad_scale

ENVO:00002149

env_local_scale

ENVO:00011764

NCBI submission package

MIGS.ba.water.6.0

depth

2m

Tax ID

3103127

num_replicons

1

geo_loc_name

Pacific Ocean: Southern California Bight, San Pedro Basin, San Pedro Ocean Time Series

env_medium

ENVO:00002149

lat_lon

33.55 N 118.4 W

BioSampleModel

MIGS.ba

ENA-FIRST-PUBLIC

2023-11-24

ENA-LAST-UPDATE

2023-12-06

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX22632949" alias="US3C007_Illumina" center_name="SUB13994642" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX22632949</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13994642">US3C007_Illumina</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Genome sequencing of strain US3C007</TITLE>
  <STUDY_REF accession="SRP473953">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP473953</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13994642">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Illumina DNA Prep kit and 10bp UDI indices</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS19630906">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS19630906</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|jozenn">US3C007</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>US3C007_Illumina</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>NextSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS19630906</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1757035</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=SRX22632949&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=SRX22632949&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="SRX22632950" alias="US3C007_Nanopore" center_name="SUB13994642" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX22632950</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13994642">US3C007_Nanopore</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Genome sequencing of strain US3C007</TITLE>
  <STUDY_REF accession="SRP473953">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP473953</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13994642">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>SQK-LSK108 1D genomic DNA ligation kit (Oxford Nanopore, UK) with slight modifications (https://doi.org/10.17504/protocols.io.bixskfne)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS19630906">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS19630906</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|jozenn">US3C007</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>US3C007_Nanopore</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WCS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</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>SRS19630906</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1757035</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=SRX22632950&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=SRX22632950&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>