Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN36504010, ERS16891220

collection_date

2022

organism

Candidatus Electrothrix sp. Rat3

env_broad_scale

ENVO:03000034

metagenomic

1

environmental-sample

1

env_local_scale

ENVO:00000045

metagenome-source

salt marsh metagenome

isolate

Rat3

NCBI submission package

MIMAG.sediment.6.0

depth

0-15 cm

elev

0

geo_loc_name

Netherlands: Rattekaai salt marsh

env_medium

ENVO:00005795

lat_lon

51.439 N 4.167 E

isolation_source

enrichment culture inoculated with sediment from salt marsh

sample-type

metagenomic assembly

sample derived-from

SAMN36436026

BioSampleModel

MIMAG.sediment

ENA-FIRST-PUBLIC

2023-10-13

ENA-LAST-UPDATE

2023-10-13

BioSample Accession(s)

SRS18389645

collection_date

2022

INSDC secondary accession

SRS18389645

NCBI submission package

Metagenome.environmental.1.0

depth

0-30 cm

organism

salt marsh metagenome

elev

0

env_broad_scale

ENVO:01000022

geo_loc_name

Netherlands: Rattekaai salt marsh

env_medium

ENVO:03000033

lat_lon

51.4372 N 4.1969 E

env_local_scale

ENVO:00000054

isolation_source

enrichment culture inoculated with sediment from salt marsh

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2023-07-22

ENA-LAST-UPDATE

2023-09-15

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX21123568" alias="Rat3ILL" center_name="SUB13699657" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21123568</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13699657">Rat3ILL</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina sequencing of Electrothrix rattekaaiensis: sediment enrichment</TITLE>
  <STUDY_REF accession="SRP450772">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP450772</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13699657">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA extraction with DNeasy PowerSoil PowerLyzer kit (Qiagen) using G2 DNA/RNA enhancer beads (Ampliqon). Nextera XT library prep.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18389645">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18389645</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN36436026</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Rat3ILL</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</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>SRS18389645</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1677259</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=SRX21123568&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=SRX21123568&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="SRX21123569" alias="Rat3NAN" center_name="SUB13699657" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21123569</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13699657">Rat3NAN</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Nanopore sequencing of Electrothrix rattekaaiensis: sediment enrichment</TITLE>
  <STUDY_REF accession="SRP450772">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP450772</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13699657">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA extraction with DNeasy PowerSoil PowerLyzer kit (Qiagen) using G2 DNA/RNA enhancer beads (Ampliqon). Size selection with BluePippin (Sage Science). SQK-LSK110 Genomic DNA by ligation protocol for nanopore prep.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18389645">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18389645</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN36436026</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Rat3NAN</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>size fractionation</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>SRS18389645</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1677259</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=SRX21123569&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=SRX21123569&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>