BioSample Accession(s)

SAMN04254521

collection_date

not applicable

note

This biosample is a metagenomic assembly obtained from the activated carbon metagenome BioSamples: SAMN04231398, SAMN04231399, SAMN04231400, and SAMN04231401.

organism

Deltaproteobacteria bacterium Ga0077550

metagenomic

TRUE

collected_by

Ameet Pinto, Univerity of Glasgow

sample_type

metagenomic assembly

environmental-sample

TRUE

metagenome-source

activated carbon metagenome

isolate

Ga0077550

NCBI submission package

Microbe.1.0

geo_loc_name

USA: Ann Arbor

env_biome

drinking water (ENVO:00003064)

lat_lon

42.2814 N 83.74829999 W

biomaterial_provider

Lutgarde Raskin, University of Michigan

isolation_source

dual media filters at the Ann Arbor, Michigan drinking water treatment plant

BioSampleModel

Microbe, viral or environmental

ENA-FIRST-PUBLIC

2015-11-10

ENA-LAST-UPDATE

2021-09-26

Samples were collected from dual media filters at the Ann Arbor, Michigan drinking water treatment plant

BioSample Accession(s)

SAMN04231398, SRS1153142

collection_date

2011-07-29

INSDC secondary accession

SRS1153142

NCBI submission package

Metagenome.environmental.1.0

source_material_id

filter media

organism

activated carbon metagenome

metagenomic

TRUE

geo_loc_name

USA: Ann Arbor

samp_mat_process

DNA extraction (bead beating, phenol chloroform purification, precipitation)

lat_lon

42.2814 N 83.74829999 W

environmental-sample

TRUE

samp_collect_device

direct collection of filter media

isolation_source

dual media filter sample 24969_A2 from the Ann Arbor, Michigan drinking water treatment plant

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2015-11-03

ENA-LAST-UPDATE

2021-09-26

Samples were collected from dual media filters at the Ann Arbor, Michigan drinking water treatment plant.

BioSample Accession(s)

SAMN04231399, SRS1153313

collection_date

2011-02-13

INSDC secondary accession

SRS1153313

NCBI submission package

Metagenome.environmental.1.0

organism

activated carbon metagenome

metagenomic

TRUE

geo_loc_name

USA: Ann Arbor

samp_mat_process

DNA extraction (bead beating, phenol chloroform purification, precipitation)

lat_lon

42.2814 N 83.74829999 W

environmental-sample

TRUE

samp_collect_device

direct collection of filter media

isolation_source

dual media filter sample 24970_A2 from the Ann Arbor, Michigan drinking water treatment plant

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2015-11-03

ENA-LAST-UPDATE

2021-09-26

Samples were collected from dual media filters at the Ann Arbor, Michigan drinking water treatment plant.

BioSample Accession(s)

SAMN04231400, SRS1153324

collection_date

2011-05-26

INSDC secondary accession

SRS1153324

NCBI submission package

Metagenome.environmental.1.0

organism

activated carbon metagenome

metagenomic

TRUE

geo_loc_name

USA: Ann Arbor

samp_mat_process

DNA extraction (bead beating, phenol chloroform purification, precipitation)

lat_lon

42.2814 N 83.74829999 W

environmental-sample

TRUE

samp_collect_device

direct collection of filter media

isolation_source

dual media filter sample 24971_A2 from the Ann Arbor, Michigan drinking water treatment plant

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2015-11-03

ENA-LAST-UPDATE

2021-09-26

Samples were collected from dual media filters at the Ann Arbor, Michigan drinking water treatment plant.

BioSample Accession(s)

SAMN04231401, SRS1153325

collection_date

2010-12-19

INSDC secondary accession

SRS1153325

NCBI submission package

Metagenome.environmental.1.0

organism

activated carbon metagenome

metagenomic

TRUE

geo_loc_name

USA: Ann Arbor

samp_mat_process

DNA extraction (bead beating, phenol chloroform purification, precipitation)

lat_lon

42.2814 N 83.74829999 W

environmental-sample

TRUE

samp_collect_device

direct collection of filter media

isolation_source

dual media filter sample 24972_A2 from the Ann Arbor, Michigan drinking water treatment plant

BioSampleModel

Metagenome or environmental

ENA-FIRST-PUBLIC

2015-11-03

ENA-LAST-UPDATE

2021-09-26

Metadata as EBI XML

<EXPERIMENT_SET>
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  <TITLE>Ann Arbor Drinking water treatment plant metagenome</TITLE>
  <STUDY_REF accession="SRP065831">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP065831</PRIMARY_ID>
      <EXTERNAL_ID namespace="BioProject">PRJNA301005</EXTERNAL_ID>
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  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was sheared to smaller fragments using the Covaris between 400bp and 550bp.  The ends are repaired, A-tailed, adapters are ligated and then PCR amplified. Library prep was performed using NEB Next DNA library prep kit.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS1153142">
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        <EXTERNAL_ID namespace="BioSample">SAMN04231398</EXTERNAL_ID>
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    <LIBRARY_DESCRIPTOR>
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      </LIBRARY_LAYOUT>
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    <SPOT_DESCRIPTOR>
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        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>102</BASE_COORD>
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      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
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</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1420149" alias="24970" center_name="University of Glasgow" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1420149</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Glasgow">24970</SUBMITTER_ID>
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  <TITLE>Ann Arbor Drinking water treatment plant metagenome</TITLE>
  <STUDY_REF accession="SRP065831">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP065831</PRIMARY_ID>
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  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was sheared to smaller fragments using the Covaris between 400bp and 550bp.  The ends are repaired, A-tailed, adapters are ligated and then PCR amplified. Library prep was performed using NEB Next DNA library prep kit.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS1153313">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS1153313</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN04231399</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
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      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
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    <SPOT_DESCRIPTOR>
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        </READ_SPEC>
        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>102</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
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  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
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    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
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    <EXPERIMENT_LINK>
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  <EXPERIMENT_ATTRIBUTES>
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Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="SRX1420172" alias="24972" center_name="University of Glasgow" broker_name="NCBI">
  <IDENTIFIERS>
    <PRIMARY_ID>SRX1420172</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of Glasgow">24972</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Ann Arbor Drinking water treatment plant metagenome</TITLE>
  <STUDY_REF accession="SRP065831">
    <IDENTIFIERS>
      <PRIMARY_ID>SRP065831</PRIMARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Genomic DNA was sheared to smaller fragments using the Covaris between 400bp and 550bp.  The ends are repaired, A-tailed, adapters are ligated and then PCR amplified. Library prep was performed using NEB Next DNA library prep kit.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="SRS1153325">
      <IDENTIFIERS>
        <PRIMARY_ID>SRS1153325</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMN04231401</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>24972_A2_filter</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED NOMINAL_LENGTH="500" NOMINAL_SDEV="0.0E0"/>
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    </LIBRARY_DESCRIPTOR>
    <SPOT_DESCRIPTOR>
      <SPOT_DECODE_SPEC>
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          <BASE_COORD>1</BASE_COORD>
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        <READ_SPEC>
          <READ_INDEX>1</READ_INDEX>
          <READ_CLASS>Application Read</READ_CLASS>
          <READ_TYPE>Reverse</READ_TYPE>
          <BASE_COORD>102</BASE_COORD>
        </READ_SPEC>
      </SPOT_DECODE_SPEC>
    </SPOT_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
    </ILLUMINA>
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  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>SRS1153325</ID>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
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    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
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</EXPERIMENT_SET>