Sample for metagenomic sequencing (Illumina) from DCME, a dichloromethane-degrading consortium, sampled on 2023/03/19.

BioSample Accession(s)

SAMN38693966, SRS20082171

collection_date

2023-03-19

INSDC secondary accession

SRS20082171

NCBI submission package

Metagenome.environmental.1.0

rel_to_oxygen

anaerobe

organism

sediment metagenome

geo_loc_name

Canada: Toronto

lat_lon

43.6 N 79.3 W

isolation_source

Sediments from a chloroalkane-contaminated site in California in 2010. Cultures have been maintained in anaerobic minimal medium ever since, with chloroform as their sole carbon and energy source until further enrichment on dichloromethane alone beginning in 2019.

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2023-12-06

ENA-LAST-UPDATE

2024-01-11

Metagenomic raw reads (pacbio) from DCME, a dichloromethane-degrading subtransfer of SC05UT, sampled on 2020/11/04.

BioSample Accession(s)

SRS18828233

collection_date

2021-11-04

INSDC secondary accession

SRS18828233

NCBI submission package

Metagenome.environmental.1.0

rel_to_oxygen

anaerobe

organism

sediment metagenome

geo_loc_name

Canada: Toronto

lat_lon

43.6 N 79.3 W

isolation_source

Sediments from a chloroalkane-contaminated site in California in 2010. Cultures have been maintained in anaerobic minimal medium ever since, with chloroform as their sole carbon and energy source until further enrichment on dichloromethane alone beginning in 2019.

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2023-10-23

ENA-LAST-UPDATE

2023-10-23

Metagenomic raw reads (Illumina) from DCME, a dichloromethane-degrading subtransfer of SC05UT, sampled on 2020/09/18.

BioSample Accession(s)

SRS18828234

collection_date

2021-09-18

INSDC secondary accession

SRS18828234

NCBI submission package

Metagenome.environmental.1.0

rel_to_oxygen

anaerobe

organism

sediment metagenome

geo_loc_name

Canada: Toronto

lat_lon

43.6 N 79.3 W

isolation_source

Sediments from a chloroalkane-contaminated site in California in 2010. Cultures have been maintained in anaerobic minimal medium ever since, with chloroform as their sole carbon and energy source until further enrichment on dichloromethane alone beginning in 2019.

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2023-10-23

ENA-LAST-UPDATE

2023-10-23

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX23130111" alias="20230319_DCME_illuminape" center_name="SUB14140519" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX23130111</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB14140519">20230319_DCME_illuminape</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina PE sequencing of DCME (2023/03/19)</TITLE>
  <STUDY_REF accession="SRP459119">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP459119</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA1013980</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was isolated from lab anaerobic enrichment cultures and sequenced using illumina NovaSeq 6000</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS20082171">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS20082171</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN38693966</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>20230319_DCME_illuminape</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>SRS20082171</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1781396</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=SRX23130111&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=SRX23130111&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="SRX21660402" alias="20201104_DCME_pacbio" center_name="SUB13778356" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21660402</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13778356">20201104_DCME_pacbio</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Pacbio sequencing of DCME (2020/11/04)</TITLE>
  <STUDY_REF accession="SRP459119">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP459119</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13778356">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was isolated from lab anaerobic enrichment cultures and sequenced using PacBio Sequel II</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18828233">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18828233</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|obulka">DCME_pacbio2021</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>20201104_DCME_pacbio</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>
    <PACBIO_SMRT>
      <INSTRUMENT_MODEL>Sequel II</INSTRUMENT_MODEL>
    </PACBIO_SMRT>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS18828233</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1707295</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=SRX21660402&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=SRX21660402&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="SRX21660400" alias="20200918_DCME_illuminape" center_name="SUB13778356" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX21660400</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB13778356">20200918_DCME_illuminape</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina PE sequencing of DCME (2020/09/18)</TITLE>
  <STUDY_REF accession="SRP459119">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP459119</PRIMARY_ID>
      <SUBMITTER_ID namespace="SUB13778356">bp0</SUBMITTER_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>DNA was isolated from lab anaerobic enrichment cultures and sequenced using illumina NovaSeq 6000</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS18828234">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS18828234</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|obulka">DCME_illumina2021</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>20200918_DCME_illuminape</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM PCR</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>SRS18828234</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1707295</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=SRX21660400&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=SRX21660400&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>