Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN46472263

collection_date

2015-02-27

metagenome_source

sediment metagenome

organism

Halarcobacter ebronensis

environmental_sample

true

env_broad_scale

missing

metagenomic

true

sample_type

missing

env_local_scale

missing

isolate

LRMN2-1

NCBI submission package

MIMAG.sediment.6.0

depth

missing

elev

missing

geo_loc_name

Spain: Catalonia, La Rapita

env_medium

missing

lat_lon

40.6404 N 0.7406 E

isolation_source

Lab-grown breviate-bacteria community

sample derived_from

SAMN40276088

BioSampleModel

MIMAG.sediment

ENA-FIRST-PUBLIC

2025-03-15

ENA-LAST-UPDATE

2025-03-15

BioSample Accession(s)

SAMN40276088, SRS20691577

collection_date

2014-02-27

INSDC secondary accession

SRS20691577

NCBI submission package

Metagenome.environmental.1.0

rel_to_oxygen

anaerobe

organism

sediment metagenome

geo_loc_name

Spain: Catalonia, La Rapita

lat_lon

40.6404 N 0.7406 E

isolation_source

mud, abandoned saltern

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2025-03-20

ENA-LAST-UPDATE

2025-03-21

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27466924" alias="LRM2N6_barcode87" center_name="SUB15027554" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27466924</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15027554">LRM2N6_barcode87</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw metagenomic sequencing reads for LRM2N6</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1084235</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was extracted from duplicate cultures grown for seven days in 3% LB-SW (45 ml) at room temperature under microaerophilic conditions. The DNA was treated with 1 mg/ml RNase A, quantified with the Qubit dsDNA HS assay kit, and stored at -20C.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691577">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691577</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276088</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LRM2N6_barcode87</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>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691577</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2060292</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX27521220" alias="LRM2N6_lib609352_8170_3" center_name="SUB15049977" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX27521220</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB15049977">LRM2N6_lib609352_8170_3</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>LRM2N6</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1084235</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Paired-end sequencing of breviate-associated bacterial communities, processed using Eurofins' INVIEW Metagenome pipeline</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691577">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691577</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN40276088</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>LRM2N6_lib609352_8170_3</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 NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS20691577</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA2065010</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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      </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=SRX27521220&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="SRX23872473" alias="lib731392_10364" center_name="SUB14156873" broker_name="NCBI">
  <IDENTIFIERS>
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    <SUBMITTER_ID namespace="SUB14156873">lib731392_10364</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>16S rRNA seq: breviate culture (LRM2N6), 1 week incubation, anoxic NO2</TITLE>
  <STUDY_REF accession="SRP493959">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP493959</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB14156873">bp0</SUBMITTER_ID>
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  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Amplicon sequencing for the 16S rRNA V4 region was executed on three biological replicates from anoxic breviate strains. DNA extraction followed the phenol-chloroform protocol. PCR amplification used 515F/806R primers with Illumina adapters, with conditions of 35 cycles and an annealing temperature of 50C. Amplified products were pooled, purified, and sequenced on a MiSeq system (2x300 bp). Initial quality control, read merging, and analysis involved Cutadapt, FLASH, and the qiime2 pipeline for denoising (DADA2), taxonomy (SILVA 138), and relative abundance assessment, excluding food source taxa.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20691577">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691577</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|viktor.tornblom@orcid">LRM2N6</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lib731392_10364</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
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  <EXPERIMENT_LINKS>
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      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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        <ID>SRA1819471</ID>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX23872499" alias="lib680275_8400" center_name="SUB14156873" broker_name="NCBI">
  <IDENTIFIERS>
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    <SUBMITTER_ID namespace="SUB14156873">lib680275_8400</SUBMITTER_ID>
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  <TITLE>16S rRNA seq: breviate culture (LRM2N6), 1 week incubation, control</TITLE>
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  <DESIGN>
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    <SAMPLE_DESCRIPTOR accession="SRS20691577">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20691577</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|viktor.tornblom@orcid">LRM2N6</SUBMITTER_ID>
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    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lib680275_8400</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
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  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
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      <XREF_LINK>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
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      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX23872500" alias="lib680276_8400" center_name="SUB14156873" broker_name="NCBI">
  <IDENTIFIERS>
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    <SUBMITTER_ID namespace="SUB14156873">lib680276_8400</SUBMITTER_ID>
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  <TITLE>16S rRNA seq: breviate culture (LRM2N6), 1 week incubation, control</TITLE>
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  <DESIGN>
    <DESIGN_DESCRIPTION>Amplicon sequencing for the 16S rRNA V4 region was executed on three biological replicates from anoxic breviate strains. DNA extraction followed the phenol-chloroform protocol. PCR amplification used 515F/806R primers with Illumina adapters, with conditions of 35 cycles and an annealing temperature of 50C. Amplified products were pooled, purified, and sequenced on a MiSeq system (2x300 bp). Initial quality control, read merging, and analysis involved Cutadapt, FLASH, and the qiime2 pipeline for denoising (DADA2), taxonomy (SILVA 138), and relative abundance assessment, excluding food source taxa.</DESIGN_DESCRIPTION>
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      <IDENTIFIERS>
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        <SUBMITTER_ID namespace="pda|viktor.tornblom@orcid">LRM2N6</SUBMITTER_ID>
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    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>lib680276_8400</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
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  <PLATFORM>
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Metadata as EBI XML

<EXPERIMENT_SET>
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  <IDENTIFIERS>
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Metadata as EBI XML

<EXPERIMENT_SET>
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