characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: INRA-CMSE

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

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text: Colmar

characteristic: city

characteristic: collection date

characteristic: common name

characteristic: depth

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: arable soil

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text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Alsace

text: A horizon

text: metagenome

text: CGAGCTCATG

text: soil metagenome

text: soil metagenome

text: Illumina

text: soil

text: 16S rRNA gene

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

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text: INRA-CMSE

characteristic: INSDC center name

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text: public

text: Colmar

unit: m

text: Soil from Colmar, sampled one year after organic waste product apllication

text: cropland biome

text: microbial feature

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unit: DD

text: Alsace

characteristic: geographic location (region and locality)

text: 12 years of organic waste application (every 2 years)

characteristic: history/previous land use

text: A horizon

characteristic: horizon

text: metagenome

characteristic: investigation type

text: CGTGTCTCTA

characteristic: multiplex identifiers

text: 5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_2 min; 35 cycles of denaturation: 94degC_30sec; annealing: 52degC_30sec; elongation: 72degC_1min; final elongation: 72degC_7min. A second PCR of 9 cycles was then conducted under similar PCR conditions with purified PCR products and ten base pair multiplex identifiers added to the primers at 5’ position to specifically identify each sample and avoid PCR biases.

characteristic: nucleic acid amplification

text: DNA was extracted using a procedure slightly modified, developed by the GenoSol platform for application in large-scale soil surveys (Terrat et al., 2012)

characteristic: nucleic acid extraction

text: Biowaste compost

characteristic: organic waste product

text: soil metagenome

characteristic: organism

text: 5ng of DNA were used for a 25 µl PCR conducted under the following conditions: initial denaturation:94degC_2.0min;35 cycles of denaturation:94degC_0.5min;annealing:52degC_0.5min;elongation:72degC_1.0min;final elongation:72degC_7.0min

characteristic: pcr conditions

text: F479:5'-CAGCMGCYGCNGTAANAC-3'; R888:5'CCGYCAATTCMTTTRAGT-3'

characteristic: pcr primers

characteristic: project name

unit: g

characteristic: sample volume or weight for DNA extraction

text: soil metagenome

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characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 16S rRNA gene

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characteristic: geographic location (elevation)

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characteristic: title


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text: cropland biome

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characteristic: geographic location (region and locality)

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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characteristic: geographic location (longitude)

text: Alsace

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characteristic: title


characteristic: ENA-CHECKLIST

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text: Biowaste compost

characteristic: organic waste product

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text: soil metagenome

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characteristic: sequencing method

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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characteristic: title


characteristic: ENA-CHECKLIST

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text: Soil from Feucherolles, sampled one year after organic waste product apllication

text: cropland biome

text: microbial feature

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text: France

text: Ile de France

characteristic: geographic location (region and locality)

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text: Compost issued from the co-composting of green wastes with sewage sludge

characteristic: organic waste product

text: soil metagenome

characteristic: organism

characteristic: pcr conditions

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text: Soil from Colmar, sampled one year after / No organic waste product apllication

characteristic: description

text: cropland biome

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: arable soil

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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text: Alsace

text: A horizon

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characteristic: title


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characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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text: Alsace

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characteristic: title


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characteristic: geographic location (country and/or sea)

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characteristic: title


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text: soil metagenome

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text: cropland biome

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Alsace

text: A horizon

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text: Farmyard manure compost

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characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: geographic location (region and locality)

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text: A horizon

characteristic: horizon

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text: Municipal solid waste compost

characteristic: organic waste product

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text: soil metagenome

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characteristic: sequencing method

text: soil

characteristic: soil environmental package

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characteristic: environment (biome)

text: microbial feature

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characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Alsace

text: A horizon

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text: Non-composted sewage sludge

text: soil metagenome

text: soil metagenome

text: Illumina

text: soil

text: 16S rRNA gene

characteristic: title


characteristic: ENA-CHECKLIST

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text: INRA-CMSE

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text: France

text: Ile de France

characteristic: geographic location (region and locality)

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text: A horizon

characteristic: horizon

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text: CGAGCTAGCT

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text: Farmyard manure

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text: soil metagenome

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characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 16S rRNA gene

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: INRA-CMSE

characteristic: INSDC center name

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text: public

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text: Feucherolles

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text: cropland biome

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: arable soil

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Ile de France

text: A horizon

text: metagenome

text: TCTCTATGCG

text: 5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_3min; 35 cycles of: denaturation: 94degC_1min; annealing: 52degC_1min; elongation: 72degC_1min, final elongation: 72degC_5min. A second PCR of 9 cycles was then conducted under similar PCR conditions with purified PCR products and ten base pair multiplex identifiers added to the primers at 5 position to specifically identify each sample and avoid PCR biases.

text: Farmyard manure

text: soil metagenome

text: 5ng of DNA were used for a 25 µl PCR conducted under the following conditions: initial denaturation:94degC_3.0min;35 cycles of denaturation:94degC_0.5min;annealing:52degC_1.0min;elongation:72degC_1.0min;final elongation:72degC_5.0min

text: FR1:5'-ANCCATTCAATCGGTANT-3';FF390:5'-CGATAACGAACGAGACCT-3'

text: soil metagenome

text: Illumina

text: soil

text: 18S rRNA gene

characteristic: title


characteristic: ENA-CHECKLIST

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text: INRA-CMSE

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text: public

text: Colmar

text: cropland biome

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vOkaSeed

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VVAG

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text: Varicella-zoster virus

text: Human herpesvirus 3

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tag: Namespace:Max Planck Institute for Molecular Genetics

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characteristic: is the sequenced pathogen host associated?

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characteristic: is the sequenced pathogen host associated?

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characteristic: collected by

text: No

text: Denmark

text: not provided

text: Sus scrofa domesticus

text: Yes

text: Escherichia coli

text: Pig caecal

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016_732_PRJ1055_Escherichia_coli_903_15070497_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_733_PRJ1055_Escherichia_coli_903_15072855_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_734_PRJ1055_Escherichia_coli_903_15069512_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016_735_PRJ1055_Escherichia_coli_903_15078473_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_736_PRJ1055_Escherichia_coli_903_15078160_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_737_PRJ1055_Escherichia_coli_903_15082398_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016_738_PRJ1055_Escherichia_coli_903_15083563_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_739_PRJ1055_Escherichia_coli_903_15083725_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Centre for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Denmark

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_740_PRJ1055_Escherichia_coli_903_15087186_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016_741_PRJ1055_Escherichia_coli_903_15087552_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_742_PRJ1055_Escherichia_coli_903_15088190_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_743_PRJ1055_Escherichia_coli_903_15090679_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016_744_PRJ1055_Escherichia_coli_903_15091884_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_745_PRJ1055_Escherichia_coli_903_15092996_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_746_PRJ1055_Escherichia_coli_903_15094218_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016_747_PRJ1055_Escherichia_coli_903_15094241_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_748_PRJ1055_Escherichia_coli_903_15094243_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_749_PRJ1055_Escherichia_coli_903_15096236_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016_750_PRJ1055_Escherichia_coli_903_15096222_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_751_PRJ1055_Escherichia_coli_903_15095645_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

text: ecoli[Unknown ST]

characteristic: strain

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_752_PRJ1055_Escherichia_coli_903_15095937_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016_753_PRJ1055_Escherichia_coli_903_15095941_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: DTU2016_754_PRJ1055_Escherichia_coli_903_15096395_1

text: DTU-GE

text: FVST / DTU

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Escherichia coli

characteristic: isolate

text: chicken meat

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

characteristic: strain

text: Ecoli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016_755_PRJ1055_Escherichia_coli_903_15096396_1

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: FVST / DTU

characteristic: collected by

text: No

text: Denmark

text: not provided

text: Gallus gallus

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Ecoli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Centre for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Denmark

text: public

text: DTU2016_756_PRJ1055_Escherichia_coli_903_15096416_1

text: DTU-GE

text: FVST / DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: host health state

text: Gallus gallus

characteristic: host scientific name

text: Yes

text: Escherichia coli

text: chicken meat

text: Escherichia coli

text: Escherichia coli

text: Ecoli