Keywords: GSC:MIxS;MIMS:5.0

BioSample Accession(s)

SAMN14825702, SRS6587282

collection_date

2018-08-29

INSDC secondary accession

SRS6587282

NCBI submission package

MIMS.me.wastewater.5.0

depth

1m

organism

activated sludge metagenome

env_broad_scale

aquatic biome [ENVO:00002030]

geo_loc_name

Denmark: Hjorring

env_medium

Activated Sludge [ENVO:00002046]

lat_lon

57.421265 N 9.975411 E

env_local_scale

Waste Water [ENVO:00002001]

isolation_source

activated sludge

BioSampleModel

MIGS/MIMS/MIMARKS.wastewater

ENA-FIRST-PUBLIC

2021-01-24

ENA-LAST-UPDATE

2021-02-28

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX8234920" alias="Hjor_18-Q3-R7-51_ILM" center_name="SUB7371278" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX8234920</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB7371278">Hjor_18-Q3-R7-51_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="SRS6587282">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS6587282</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|caitlin_singleton">Hjor_18-Q3-R7-51</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Hjor_18-Q3-R7-51_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>SRS6587282</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=SRX8234920&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=SRX8234920&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="SRX8234968" alias="Hjor_18-Q3-R7-51_NP" center_name="SUB7371278" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX8234968</PRIMARY_ID>
    <SUBMITTER_ID namespace="SUB7371278">Hjor_18-Q3-R7-51_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="SRS6587282">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS6587282</PRIMARY_ID>
        <SUBMITTER_ID namespace="pda|caitlin_singleton">Hjor_18-Q3-R7-51</SUBMITTER_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Hjor_18-Q3-R7-51_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>SRS6587282</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=SRX8234968&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=SRX8234968&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>