Genome sequencing of an Endozoicomonas strain to study the core and pangenomes of soil and plant-associated prokaryotes

BioSample Accession(s)

SAMN39945184, SRS20538312

biome

missing

collection_date

missing

feature

missing

geo_loc_name

Portugal: Lisbon Oceanarium

host

not applicable

isol_growth_condt

missing

isolation_source

missing

lat_lon

38.7636 N 9.09365 W

material

missing

num_replicons

missing

ref_biomaterial

missing

strain

NE40

type-material

type strain of Endozoicomonas lisbonensis

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX23708321" alias="JGI-SRA-225280" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX23708321</PRIMARY_ID>
    <EXTERNAL_ID namespace="JGI">JGI-SRA-225280</EXTERNAL_ID>
    <SUBMITTER_ID namespace="">JGI-SRA-225280</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Endozoicomonas sp. NE40</TITLE>
  <STUDY_REF accession="SRP491227">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP491227</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1075804</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS20538312">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20538312</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN39945184</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>NYWHB</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Low Input (DNA)</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <PACBIO_SMRT>
      <INSTRUMENT_MODEL>Revio</INSTRUMENT_MODEL>
    </PACBIO_SMRT>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20538312</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1806608</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=SRX23708321&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=SRX23708321&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="SRX23708322" alias="JGI-SRA-225281" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX23708322</PRIMARY_ID>
    <EXTERNAL_ID namespace="JGI">JGI-SRA-225281</EXTERNAL_ID>
    <SUBMITTER_ID namespace="">JGI-SRA-225281</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Endozoicomonas sp. NE40</TITLE>
  <STUDY_REF accession="SRP491227">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP491227</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1075804</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION/>
    <SAMPLE_DESCRIPTOR accession="SRS20538312">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20538312</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN39945184</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>NYWHB</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Low Input (DNA)</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <PACBIO_SMRT>
      <INSTRUMENT_MODEL>Revio</INSTRUMENT_MODEL>
    </PACBIO_SMRT>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20538312</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1806608</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=SRX23708322&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=SRX23708322&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>