This BioSample is a metagenomic assembly obtained from the Lyne_18-Q3-R50-59 metagenome BioSample: SAMN14825708.

BioSample Accession(s)

SAMN16426249

collection_date

2018-08-29

organism

Dehalococcoidia bacterium

env_broad_scale

aquatic biome [ENVO:00002030]

metagenomic

1

derived-from

This BioSample is a metagenomic assembly obtained from the Lyne_18-Q3-R50-59 activated sludge metagenome BioSample: SAMN14825708.

environmental-sample

1

env_local_scale

Waste Water [ENVO:00002001]

metagenome-source

activated sludge metagenome

isolate

Lyne_18-Q3-R50-59_MAXAC.019

NCBI submission package

MIMAG.wastewater.5.0

geo_loc_name

Denmark: Lynetten

env_medium

Activated Sludge [ENVO:00002046]

lat_lon

55.695362 N 12.612702 E

isolation_source

activated sludge from Lyne_18-Q3-R50-59

sample-type

metagenomic assembly

BioSampleModel

MIMAG.wastewater

ENA-FIRST-PUBLIC

2021-01-20

ENA-LAST-UPDATE

2021-02-28

Keywords: GSC:MIxS;MIMS:6.0

BioSample Accession(s)

SAMN14825708, SRS6587289

collection_date

2018-08-29

INSDC secondary accession

SRS6587289

NCBI submission package

MIMS.me.wastewater.6.0

depth

1m

organism

activated sludge metagenome

env_broad_scale

aquatic biome [ENVO:00002030]

geo_loc_name

Denmark: Lynetten

env_medium

Activated Sludge [ENVO:00002046]

lat_lon

55.695362 N 12.612702 E

env_local_scale

Waste Water [ENVO:00002001]

isolation_source

activated sludge from wastewater treatment plant

BioSampleModel

MIGS/MIMS/MIMARKS.wastewater

ENA-FIRST-PUBLIC

2021-01-24

ENA-LAST-UPDATE

2022-08-10

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX8234927" alias="Lyne_18-Q3-R50-59_ILM" center_name="SUB7371278" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX8234927</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB7371278">Lyne_18-Q3-R50-59_ILM</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Illumina sequencing of activated sludge metagenome</TITLE>
  <STUDY_REF accession="SRP259711">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP259711</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA629478</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Library preparation and sequencing was conducted at Admera Health. Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit of Illumina with insert size targets of 300-400 bp PE data.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS6587289">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS6587289</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|caitlin_singleton">Lyne_18-Q3-R50-59</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Lyne_18-Q3-R50-59_ILM</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>HiSeq X Ten</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS6587289</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1071489</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=SRX8234927&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=SRX8234927&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="SRX8234970" alias="Lyne_18-Q3-R50-59_NP" center_name="SUB7371278" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX8234970</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB7371278">Lyne_18-Q3-R50-59_NP</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Nanopore sequencing of activated sludge metagenome</TITLE>
  <STUDY_REF accession="SRP259711">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP259711</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA629478</EXTERNAL_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Library preparation and sequencing was conducted at Aalborg University, following the Oxford Nanopore 1D Genomic DNA by ligation SQK-LSK109 protocol and run on PromethION R9 FLO-PRO002 flow cells.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS6587289">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS6587289</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|caitlin_singleton">Lyne_18-Q3-R50-59</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Lyne_18-Q3-R50-59_NP</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>PromethION</INSTRUMENT_MODEL>
    </OXFORD_NANOPORE>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS6587289</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>SRA1071489</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=SRX8234970&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=SRX8234970&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>