Keywords: GSC:MIxS;MIMAG:6.0

BioSample Accession(s)

SAMN22164178, ERS20171535

type-material

reference material of Candidatus Liberimonas magnetica

organism

Candidatus Liberimonas magnetica

collection date

2017-07-26

isolation source

bog soil from slope of Durykino raven

env_broad_scale

Terrestrial biome

geo loc name

Russia: Moscow Region, Durykino ravine

metagenomic

1

environmental sample

1

metagenome source

soil metagenome

env_local_scale

Peaty bog soil

isolate

DUR002

NCBI submission package

MIMAG.soil.6.0

depth

10 cm

lat lon

56.048889 N 37.164722 E

elev

100 m

env_medium

Bog soil

sample-type

metagenomic assembly

sample derived-from

SAMN22133373

BioSampleModel

MIMAG.soil

ENA-FIRST-PUBLIC

2021-10-08

ENA-LAST-UPDATE

2024-05-26

BioSample Accession(s)

SAMN22133373, SRS10477292

collection_date

2017-07-26

INSDC secondary accession

SRS10477292

NCBI submission package

Metagenome.environmental.1.0

depth

10 cm

organism

soil metagenome

geo_loc_name

Russia: Moscow Region, Durykino ravine

lat_lon

56.048889 N 37.164722 E

isolation_source

bog soil from slope of Durykino raven

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2021-10-07

ENA-LAST-UPDATE

2021-10-12

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX12515544" alias="DUR_short" center_name="SUB10498793" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX12515544</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB10498793">DUR_short</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>SRA of Durykino ravine metagenome (short reads)</TITLE>
  <STUDY_REF accession="SRP340409">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP340409</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB10498793">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA sequencing was conducted using the DNBSEQ (MGI)</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS10477292">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS10477292</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|uzunmasha">Durykino ravine metagenome</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>DUR_short</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>
    <DNBSEQ>
      <INSTRUMENT_MODEL>DNBSEQ-G400</INSTRUMENT_MODEL>
    </DNBSEQ>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS10477292</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1307574</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=SRX12515544&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=SRX12515544&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="SRX12515545" alias="DUR_long" center_name="SUB10498793" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX12515545</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB10498793">DUR_long</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>SRA of Durykino ravine metagenome (long reads)</TITLE>
  <STUDY_REF accession="SRP340409">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP340409</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB10498793">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing was used for ONT sequencing libraries preparation.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS10477292">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS10477292</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|uzunmasha">Durykino ravine metagenome</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>DUR_long</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</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>SRS10477292</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1307574</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=SRX12515545&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=SRX12515545&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="SRX15148787" alias="DurMag" center_name="SUB11427772" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX15148787</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB11427772">DurMag</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>SRA of Durykino ravine soil metagenome 16S rRNA sequencing after magnetic enrichment</TITLE>
  <STUDY_REF accession="SRP340409">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP340409</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA769424</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Metagenomic 16S rRNA sequencing was conducted using the Illumina MiSeq platform</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS10477292">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS10477292</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN22133373</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>DurMag</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>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS10477292</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1414609</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=SRX15148787&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=SRX15148787&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>