text: public

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text: DTU-GE

text: DTU

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: imported food

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: E.coli

text: imported food

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

text: colistin resistance


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

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characteristic: External Id

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characteristic: Submitter Id

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characteristic: broker name

text: DTU

characteristic: description

text: No

text: Denmark

characteristic: geographic location (country and/or sea)

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text: imported food

text: Yes

text: E.coli

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characteristic: organism

text: Escherichia coli

text: colistin resistance

characteristic: title


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characteristic: environmental sample

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characteristic: geographic location (latitude)

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characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

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characteristic: INSDC status

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characteristic: is the sequenced pathogen host associated?

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characteristic: INSDC status

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text: Yes

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characteristic: SRA accession

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characteristic: title


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characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (latitude)

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characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: E.coli

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characteristic: isolation source host associated

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characteristic: INSDC status

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text: Denmark

text: imported food

text: Yes

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text: public

characteristic: SRA accession

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characteristic: description

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characteristic: geographic location (country and/or sea)

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characteristic: isolate

text: imported food

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text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (latitude)

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characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

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characteristic: isolation source host associated

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text: Denmark

text: imported food

text: Yes

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text: public

characteristic: SRA accession

text: DTU2016-233-PRJ1054-Escherichia-coil-2012-70-468-33_S23_L001

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text: DTU-GE

characteristic: broker name

text: DTU

characteristic: description

text: No

text: Denmark

characteristic: geographic location (country and/or sea)

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text: imported food

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characteristic: title


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text: DTU2016-234-PRJ1054-Escherichia-coil-2012-70-473-41_S24_L001

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characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: E.coli

text: imported food

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

text: colistin resistance


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text: public

characteristic: INSDC status

text: DTU2016-235-PRJ1054-Escherichia-coil-2012-70-473-75_S25_L001

text: DTU-GE

text: DTU

text: No

text: Denmark

text: imported food

text: Yes

text: E.coli

text: imported food

text: Escherichia coli

text: Escherichia coli

text: colistin resistance


text: public

characteristic: SRA accession

text: DTU2016-236-PRJ1054-Escherichia-coil-2012-70-506-35_S26_L001

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: DTU

characteristic: description

text: No

text: Denmark

characteristic: geographic location (country and/or sea)

text: imported food

text: Yes

text: E.coli

characteristic: isolate

text: imported food

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: colistin resistance

characteristic: title


text: public

text: DTU2016-237-PRJ1054-Escherichia-coil-2013-70-368-4_S27_L001

text: DTU-GE

text: DTU

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: imported food

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: E.coli

text: imported food

characteristic: isolation source host associated

text: Escherichia coli

text: Escherichia coli

text: colistin resistance


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: DTU2016-185-PRJ1054-Salmonella-Not-typeable-2008-60-1169-2_S1_L001

text: DTU-GE

text: DTU

text: No

text: Germany

text: Poultry

text: Yes

text: Salmonella enterica

text: imported food

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

characteristic: serovar

text: colistin resistance


text: public

characteristic: SRA accession

text: DTU2016-186-PRJ1054-Salmonella-Not-typeable-2008-60-1169-5_S2_L001

characteristic: Submitter Id

text: DTU-GE

characteristic: broker name

text: DTU

characteristic: collected by

characteristic: description

text: No

text: Germany

characteristic: geographic location (country and/or sea)

text: Poultry

text: Yes

text: Salmonella enterica

characteristic: isolate

text: imported food

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016-187-PRJ1054-Salmonella-Not-typeable-2008-60-1169-8_S3_L001

text: DTU-GE

text: DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Poultry

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Salmonella enterica

text: imported food

characteristic: isolation source host associated

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016-188-PRJ1054-Salmonella-Not-typeable-2008-60-1169-9_S4_L001

characteristic: Submitter Id

text: DTU-GE

text: DTU

text: No

text: Germany

text: Poultry

text: Yes

text: Salmonella enterica

text: imported food

text: Salmonella enterica

text: Salmonella enterica

text: II [1],4,[5],12,[27]:b:[e,n,x] or Schleissheim (Schleissheim is extremely rare)

characteristic: serovar

text: colistin resistance


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016-189-PRJ1054-Salmonella-Bovismorbifican-2009-60-589-1_S5_L001

text: DTU-GE

characteristic: broker name

text: DTU

characteristic: collected by

characteristic: description

text: No

text: Germany

characteristic: geographic location (country and/or sea)

text: Turkey

text: Yes

text: Salmonella enterica

characteristic: isolate

text: imported food

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Hindmarsh or Bovismorbificans

text: colistin resistance

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016-190-PRJ1054-Salmonella-4-12-2010-60-2870-1_S6_L001

text: DTU-GE

text: DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Poultry

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Salmonella enterica

text: imported food

characteristic: isolation source host associated

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016-191-PRJ1054-Salmonella-Paratyphi-B-var-Java-2011-60-1117-1_S7_L001

characteristic: Submitter Id

text: DTU-GE

text: DTU

text: No

text: Germany

text: Poultry

text: Yes

text: Salmonella enterica

text: imported food

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

characteristic: serovar

text: colistin resistance


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016-192-PRJ1054-Salmonella-Paratyphi-B-var-Java-2011-60-1117-3_S8_L001

text: DTU-GE

characteristic: broker name

text: DTU

characteristic: collected by

characteristic: description

text: No

text: Germany

characteristic: geographic location (country and/or sea)

text: Poultry

text: Yes

text: Salmonella enterica

characteristic: isolate

text: imported food

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: colistin resistance

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016-193-PRJ1054-Salmonella-4-12-b-2011-60-1117-4_S9_L001

text: DTU-GE

text: DTU

characteristic: collection date

text: No

characteristic: environmental sample

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Poultry

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Salmonella enterica

text: imported food

characteristic: isolation source host associated

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: DTU2016-194-PRJ1054-Salmonella-Paratyphi-B-var-Java-2011-60-1117-10_S10_L001

characteristic: Submitter Id

text: DTU-GE

text: DTU

text: No

text: Germany

text: Poultry

text: Yes

text: Salmonella enterica

text: imported food

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

characteristic: serovar

text: colistin resistance


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: DTU2016-195-PRJ1054-Salmonella-Paratyphi-B-var-Java-2013-60-1930-1_S11_L001

text: DTU-GE

characteristic: broker name

text: DTU

characteristic: collected by

characteristic: description

text: No

text: Germany

characteristic: geographic location (country and/or sea)

text: Poultry

text: Yes

text: Salmonella enterica

characteristic: isolate

text: imported food

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: DTU2016-196-PRJ1054-Salmonella-Paratyphi-B-var-Java-F14-868-1_S12_L001

text: DTU-GE

text: DTU

characteristic: collection date

text: F14-868-1, The collection date of this isolate is unknown NOT 2013.

text: No

characteristic: environmental sample

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Yes

characteristic: is the sequenced pathogen host associated?

text: Salmonella enterica

text: imported food

characteristic: isolation source host associated

text: Salmonella enterica

text: Salmonella enterica

text: Paratyphi B

text: colistin resistance


characteristic: ENA-CHECKLIST

text: WEIZMANN INSTITUTE OF SCIENCE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:WEIZMANN INSTITUTE OF SCIENCE

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: RNAseq


characteristic: ENA-FIRST-PUBLIC

text: MYCOBT

text: public

text: uncultured fungus

text: A horizon

characteristic: description

text: Spruce forest

characteristic: environment (biome)

text: forest

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

characteristic: investigation type

text: uncultured fungus

characteristic: organism

text: Solling

characteristic: project name

text: uncultured fungus

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MYCOBT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: collection date

text: uncultured fungus

text: B horizon

text: Spruce forest

text: forest

text: soil

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: uncultured fungus

text: Solling

text: uncultured fungus

text: Illumina

text: soil


characteristic: ENA-FIRST-PUBLIC

text: MYCOBT

text: public

characteristic: Submitter Id

text: uncultured fungus

characteristic: common name

text: Oa layer

characteristic: description

text: Spruce forest

characteristic: environment (biome)

text: forest

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

characteristic: investigation type

text: uncultured fungus

text: Solling

text: uncultured fungus

text: Illumina

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MYCOBT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: uncultured fungus

text: Oe layer

text: Spruce forest

text: forest

text: soil

text: Germany

text: metagenome

text: uncultured fungus

characteristic: organism

text: Solling

characteristic: project name

text: uncultured fungus

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: PASTEUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmonella enterica subsp. enterica serovar Enteritidis


text: MPICE

text: public

text: RNA isolated from feeding cavity of mouse carcass with actively feeding Nicrophorus larvae

characteristic: description

text: Nicrophorus vespilloides

text: Nicrophorus vespilloides

text: Carcass Feeding Caviity


text: CBS

text: public

text: Fusarium proliferatum ITEM2287

text: Fusarium proliferatum

text: Fusarium proliferatum

text: Fusarium proliferatum ITEM2287


text: CBS

text: public

text: Fusarium proliferatum ITEM2400

text: Fusarium proliferatum

text: Fusarium proliferatum

text: Fusarium proliferatum ITEM2400


text: CBS

text: public

text: Fusarium graminearum PH-1

text: Fusarium graminearum PH-1

text: Fusarium graminearum PH-1


text: CBS

text: public

text: Fusarium oxysporum

text: Fusarium oxysporum

text: Fusarium oxysporum f. sp. cumini F11


text: CBS

text: public

text: Fusarium oxysporum

text: Fusarium oxysporum

text: Fusarium oxysporum f. sp. dianthi Fod001


text: CBS

text: public

text: Fusarium oxysporum

text: Fusarium oxysporum

text: Fusarium oxysporum f. sp. dianthi Fod008


text: CBS

text: public

text: Pooled sequencing of 5 Fusarium graminearum strains

text: Fusarium graminearum

text: Fusarium graminearum


text: UCSDMI

text: public

text: pH 4.5 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 4.5 year 2006

text: TRUE

characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

characteristic: env feature

text: soil

characteristic: env package

text: soil

text: TRUE

characteristic: extracted DNA avail now

text: Scotland:Craibstone

characteristic: geo loc name

characteristic: host subject id

characteristic: latitude

characteristic: longitude

text: soil metagenome

characteristic: ph

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

characteristic: public

text: completed

text: soil

characteristic: sample type

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: pH 4.5 year 2007

text: pH 4.5 year 2007

text: TRUE

text: cropland biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

text: soil metagenome

characteristic: organism

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

characteristic: title

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: UCSDMI

text: public

characteristic: Submitter Id

text: pH 5.0 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 5.0 year 2006

characteristic: description

text: TRUE

characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

characteristic: env feature

text: soil

characteristic: env package

text: soil

text: TRUE

characteristic: extracted DNA avail now

text: Scotland:Craibstone

characteristic: geo loc name

characteristic: host subject id

text: soil metagenome

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pH 5.0 year 2007

text: pH 5.0 year 2007

text: TRUE

text: cropland biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

characteristic: latitude

characteristic: longitude

text: soil metagenome

characteristic: ph

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

characteristic: public

text: completed

text: soil

characteristic: sample type

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pH 5.5 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 5.5 year 2006

characteristic: description

text: TRUE

characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

text: soil metagenome

characteristic: organism

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

characteristic: title

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pH 5.5 year 2007

text: pH 5.5 year 2007

text: TRUE

text: cropland biome

text: agricultural soil

characteristic: env feature

text: soil

characteristic: env package

text: soil

text: TRUE

characteristic: extracted DNA avail now

text: Scotland:Craibstone

characteristic: geo loc name

characteristic: host subject id

text: soil metagenome

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pH 6.0 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 6.0 year 2006

text: TRUE

text: cropland biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

characteristic: latitude

characteristic: longitude

text: soil metagenome

characteristic: ph

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

characteristic: public

text: completed

text: soil

characteristic: sample type

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pH 6.0 year 2007

text: pH 6.0 year 2007

characteristic: description

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characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

text: soil metagenome

characteristic: organism

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

characteristic: title

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pH 6.5 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 6.5 year 2006

text: TRUE

text: cropland biome

text: agricultural soil

characteristic: env feature

text: soil

characteristic: env package

text: soil

text: TRUE

characteristic: extracted DNA avail now

text: Scotland:Craibstone

characteristic: geo loc name

characteristic: host subject id

text: soil metagenome

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

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text: Missing: Not provided


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characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pH 6.5 year 2007

text: pH 6.5 year 2007

text: TRUE

text: cropland biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

characteristic: latitude

characteristic: longitude

text: soil metagenome

characteristic: ph

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

characteristic: public

text: completed

text: soil

characteristic: sample type

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

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text: Missing: Not provided


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pH 7.0 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 7.0 year 2006

characteristic: description

text: TRUE

characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

text: soil metagenome

characteristic: organism

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

characteristic: title

text: Effect of soil pH on soil metagenome

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text: Missing: Not provided

text: Missing: Not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pH 7.0 year 2007

text: pH 7.0 year 2007

text: TRUE

text: cropland biome

text: agricultural soil

characteristic: env feature

text: soil

characteristic: env package

text: soil

text: TRUE

characteristic: extracted DNA avail now

text: Scotland:Craibstone

characteristic: geo loc name

characteristic: host subject id

text: soil metagenome

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pH 7.5 year 2006

characteristic: anonymized name

characteristic: depth

text: pH 7.5 year 2006

text: TRUE

text: cropland biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

characteristic: latitude

characteristic: longitude

text: soil metagenome

characteristic: ph

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

characteristic: public

text: completed

text: soil

characteristic: sample type

text: sequenced (16S)

text: soil metagenome

text: Effect of soil pH on soil metagenome

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text: UCSDMI

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text: public

text: pH 7.5 year 2007

text: pH 7.5 year 2007

characteristic: description

text: TRUE

characteristic: elevation

text: cropland biome

characteristic: env biome

text: agricultural soil

text: soil

text: soil

text: TRUE

text: Scotland:Craibstone

text: soil metagenome

characteristic: organism

text: Missing: Not provided

text: LBNL

text: FALSE

text: TRUE

text: completed

text: soil

text: sequenced (16S)

text: soil metagenome

characteristic: title

text: Effect of soil pH on soil metagenome

text: Missing: Not provided

text: Missing: Not provided

text: Missing: Not provided


text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 16S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

text: Miseq sequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 12-year (0-10 cm soil layer)


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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

text: metagenome

text: bacterial mixed RNA library

characteristic: organism

text: 17S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 12-year (0-10 cm soil layer)

characteristic: title


text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: bacterial mixed RNA library

text: 18S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 12-year (0-10 cm soil layer)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 19S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

text: Miseq sequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 12-year (10-20 cm soil layer)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: alpine meadowed

text: artificial grassland

text: soil

text: China

text: metagenome

text: bacterial mixed RNA library

characteristic: organism

text: 20S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 12-year (10-20 cm soil layer)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: bacterial mixed RNA library

text: 21S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 12-year (10-20 cm soil layer)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 22S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

text: Miseq sequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 8-year (0-10 cm soil layer)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: alpine meadowed

text: artificial grassland

text: soil

text: China

text: metagenome

text: bacterial mixed RNA library

characteristic: organism

text: 23S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 8-year (0-10 cm soil layer)

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

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text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

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text: 24S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 25S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

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characteristic: sequencing method

text: soil

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text: 8-year (10-20 cm soil layer)


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characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

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text: public

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characteristic: SRA accession

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characteristic: organism

text: 26S rRNA sequencing

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text: Miseq sequencing

text: soil

text: 8-year (10-20 cm soil layer)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: bacterial mixed RNA library

text: 27S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 8-year (10-20 cm soil layer)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 28S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

text: Miseq sequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 4-year (0-10 cm soil layer)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: alpine meadowed

text: artificial grassland

text: soil

text: China

text: metagenome

text: bacterial mixed RNA library

characteristic: organism

text: 29S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 4-year (0-10 cm soil layer)

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: bacterial mixed RNA library

text: 30S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 4-year (0-10 cm soil layer)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

text: alpine meadowed

text: artificial grassland

text: soil

text: China

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: bacterial mixed RNA library

text: 31S rRNA sequencing

characteristic: project name

text: bacterial mixed RNA library

text: Miseq sequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: 4-year (10-20 cm soil layer)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: alpine meadowed

text: artificial grassland

text: soil

text: China

text: metagenome

text: bacterial mixed RNA library

characteristic: organism

text: 32S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 4-year (10-20 cm soil layer)

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SOUTHWEST UNIVERSITY FOR NATIONALITIES

text: public

characteristic: Submitter Id

characteristic: collection date

text: alpine meadowed

characteristic: environment (biome)

text: artificial grassland

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: bacterial mixed RNA library

text: 33S rRNA sequencing

text: bacterial mixed RNA library

text: Miseq sequencing

text: soil

text: 4-year (10-20 cm soil layer)


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PASTEUR

text: public


characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Wadsworth Center, New York State Department of Health

text: ArrayExpress

characteristic: broker name

text: Protocols: E. coli strain RPB104 (MG1655 with C-terminally SPA-tagged rpoS) was grown overnight in M9 minimal medium with 0.4% glycerol at 30 degrees C and then subcultured 1:100 in the same medium, and grown for 60 hours to saturation (OD600 of about 3). Cultures were crosslinked by adding formaldehyde to a final concentration of 1%, incubated for 20 minutes at room temperature, and quenched by adding glycine to a final concentration of 0.5 M. Cells were washed once in original culture volume of 1X TBS then washed again in 1 mL of 1X TBS. The supernatant was removed and the pellet was stored at -20 degrees C. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, and then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 2 uL anti-FLAG antibody (M2) were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150 mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10 ul 10x quick blunting buffer, 10 ul dNTP mix (kit supplied), 80 ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3’->5’exo-), from NEB: The samples were resuspended in the following mixture: 10 ul 10X NEBuffer 2, 2 ul 100mM dATP (NEB), 88 ul dH2O, 2 ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100 ul 1x ligase buffer (50 ul 2x buffer + 50 ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR with Illumina primers 1.1 and 2.1 (1 uM ea). The manual ct was set to 0.1 and 3 was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number of : 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. The following 50ul PCR reaction was used: 5 ul 10x Taq buffer, 8 ul ChIP DNA with ligated adapters, 1.0 ul Illumina primer 1.1 (100 uM), 1.0 ul Illumina primer 2.1 (100 uM), 0.4 ul dNTP mix (25 mM each), 1.5 ul taq, 33.6 ul dH2O. The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200 bp to 500 bp was cut out and gel purified. The barcoded libraries were quantified using Qubit and pooled at equimolar concentrations. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, and then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 2 uL anti-FLAG antibody (M2) were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150 mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10 ul 10x quick blunting buffer, 10 ul dNTP mix (kit supplied), 80 ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3’->5’exo-), from NEB: The samples were resuspended in the following mixture: 10 ul 10X NEBuffer 2, 2 ul 100mM dATP (NEB), 88 ul dH2O, 2 ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150 mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100 ul 1x ligase buffer (50 ul 2x buffer + 50 ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR with Illumina primers 1.1 and 2.1 (1 uM ea). The manual ct was set to 0.1 and 3 was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number of : 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. The following 50ul PCR reaction was used: 5 ul 10x Taq buffer, 8 ul ChIP DNA with ligated adapters, 1.0 ul Illumina primer 1.1 (100 uM), 1.0 ul Illumina primer 2.1 (100 uM), 0.4 ul dNTP mix (25 mM each), 1.5 ul taq, 33.6 ul dH2O. The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200 bp to 500 bp was cut out and gel purified. The barcoded libraries were quantified using Qubit and pooled at equimolar concentrations.

characteristic: description

text: expression of C-terminally SPA-tagged rpoS

characteristic: genotype

text: Escherichia coli str. K-12 substr. MG1655


text: Wadsworth Center, New York State Department of Health

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSTITUT PASTEUR

text: public

tag: Namespace:INSTITUT PASTEUR

characteristic: Submitter Id

characteristic: collection date

text: Angola

text: Disease

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Streptococcus agalactiae

text: Streptococcus agalactiae

characteristic: strain

text: CC17 strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Homo sapiens

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: CC17 strain


text: INSTITUT PASTEUR

characteristic: INSDC last update

text: public

text: France

characteristic: geographic location (country and/or sea)

text: Disease

text: Homo sapiens

text: Blood

characteristic: isolation source

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: CC17 strain


text: INSTITUT PASTEUR

text: public

characteristic: INSDC status

characteristic: SRA accession

text: France

text: Disease

text: Homo sapiens

text: CSF

text: Streptococcus agalactiae

characteristic: organism

text: Streptococcus agalactiae

text: CC17 strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: GOF18-EGFP EpiSC (E3) were maintained in a 1:1 mixture of mouse embryonic fibroblast-conditioned media (MEF-CM) containing 20% KnockOut Serum Replacement (KSR) supplemented with 10 ng/ml FGF2 and N2B27 supplemented with 10 ng/ml FGF2 and 10 ng/ml Activin A (CM/N2B27+FA) on fetal bovine serum (FBS)-coated dishes. For EB formation, 3,000 cells were seeded into 96-well V-bottom plates in DMEM containing 10% FBS, 0.1% poly(vinyl alcohol), and 5 μM Y-27632. On days 1-5, 16 EBs were pooled and total RNA was isolated using the RNeasy Mini Kit (QIAGEN) with on-column DNase treatment. Sequencing libraries were prepared according to the TruSeq RNA Sample Preparation protocol (Illumina) with poly-A selection.

characteristic: description

characteristic: genotype

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: 10% FBS (EB)

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: Paenibacillus macerans

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Paenibacillus macerans

text: Paenibacillus macerans

text: Paenibacillus macerans

characteristic: strain


text: Mycobacterium fortuitum

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Mycobacterium fortuitum

text: Mycobacterium fortuitum

characteristic: organism

text: Mycobacterium fortuitum


text: Bacillus subtilis

text: SC

text: public

text: Bacillus subtilis

characteristic: common name

text: Bacillus subtilis

text: Bacillus subtilis


text: Streptococcus sanguinis

text: SC

text: public

text: Streptococcus sanguinis

text: Streptococcus sanguinis

text: Streptococcus sanguinis


text: Chromobacterium violaceum

text: SC

text: public

text: Chromobacterium violaceum

text: Chromobacterium violaceum

text: Chromobacterium violaceum


text: Moraxella bovis

text: SC

text: public

text: Moraxella bovis

text: Moraxella bovis

text: Moraxella bovis


E-MTAB-5342:Esrrb, 0 h

text: public

text: E-MTAB-5342:Esrrb, 0 h

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

characteristic: cell type

text: house mouse

text: Protocols: Tet-on Esrrb EpiSCs (GOF18-E3 EpiSCs carrying the Tet-on-Esrrb-IRES-Venus and Pou5f1 [3.5 kb upstream of the TSS]-IRES-Puro transgenes) were maintained in mouse embryonic fibroblast-conditioned media (MEF-CM) containing 20% KnockOut Serum Replacement (KSR) supplemented with 10 ng/ml FGF2 (CM+FGF2) on fetal bovine serum (FBS)-coated dishes. For reprogramming, Tet-on Esrrb EpiSCs were dissociated into single cells using Accutase and plated in CM+FGF2 supplemented with 5 μM Y-27632 on FBS-coated dishes. After overnight culture, the medium was replaced by DMEM/F12 containing 10% KSR supplemented with LIF, 2i (1 μM PD0325901 and 3 μM CHIR99021), and 1 μg/ml Dox. Cells were harvested and cross-linked with 1% formaldehyde in PBS for 10 min at room temperature, and chromatin was sheared using Diagenode Bioruptor (high power, 40 cycles of 30 sec on and 30 sec off) equipped with a water-cooling system (4°C) in sonication buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.5% SDS) supplemented with 1× protease inhibitor cocktail (Sigma). Sheared chromatin with an average fragment size of 200-300 bp was immunoprecipitated in 4× volume of ChIP dilution buffer (10 mM Tris-HCl [pH 8.0], 125 mM NaCl, 0.125% sodium deoxycholate, 1.25% Triton X-100) using Dynabeads protein A or G coupled with the following primary antibodies: mouse anti-Esrrb (PP-H6705-00, R&D Systems); rabbit anti-Nanog (A300-397A, Bethyl Laboratories); goat anti-Oct4 (sc-8628, Santa Cruz); goat anti-Sox2 (GT15098, Neuromics). Beads were washed once with low-salt buffer (20 mM, Tris-HCl [pH 8.0], 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), twice with high-salt buffer (20 mM, Tris-HCl [pH 8.0], 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), twice with RIPA buffer (50 mM, Hepes-KOH [pH 7.6], 250 mM LiCl, 1 mM EDTA, 1% Igepal CA630, 0.7% sodium deoxycholate), and once with TE containing 50 mM NaCl. After incubation with elution buffer (10 mM, Tris-HCl [pH 8.0], 300 mM NaCl, 5 mM EDTA, 0.5% SDS), immunoprecipitated and input DNA were reverse cross-linked and purified. Sequencing libraries were prepared according to the TruSeq ChIP Sample Preparation protocol (Illumina) with size selection of 250-450 bp.

characteristic: description

text: Esrrb-tet-on

characteristic: genotype

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb, 0 h


E-MTAB-5342:Esrrb, 24 h

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5342:Esrrb, 24 h

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb, 24 h

characteristic: title


E-MTAB-5342:Esrrb, 48 h

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5342:Esrrb, 48 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb, 48 h


E-MTAB-5342:Esrrb, 72 h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5342:Esrrb, 72 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb, 72 h


E-MTAB-5342:Esrrb, 8 h

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5342:Esrrb, 8 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Esrrb, 8 h


E-MTAB-5342:Input, 0 h

text: public

text: E-MTAB-5342:Input, 0 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

characteristic: common name

text: Esrrb-tet-on

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Input, 0 h


E-MTAB-5342:Input, 24 h

text: public

text: E-MTAB-5342:Input, 24 h

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

characteristic: cell type

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Input, 24 h


E-MTAB-5342:Input, 48 h

text: public

text: E-MTAB-5342:Input, 48 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

characteristic: description

text: Esrrb-tet-on

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Input, 48 h


E-MTAB-5342:Input, 72 h

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5342:Input, 72 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Input, 72 h


E-MTAB-5342:Input, 8 h

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5342:Input, 8 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Input, 8 h


E-MTAB-5342:Nanog, 0 h

text: public

text: E-MTAB-5342:Nanog, 0 h

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nanog, 0 h

characteristic: title


E-MTAB-5342:Nanog, 24 h

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5342:Nanog, 24 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nanog, 24 h


E-MTAB-5342:Nanog, 48 h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5342:Nanog, 48 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nanog, 48 h


E-MTAB-5342:Nanog, 72 h

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5342:Nanog, 72 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Nanog, 72 h


E-MTAB-5342:Nanog, 8 h

text: public

text: E-MTAB-5342:Nanog, 8 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

characteristic: common name

text: Esrrb-tet-on

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Nanog, 8 h


E-MTAB-5342:Oct4, 0 h

text: public

text: E-MTAB-5342:Oct4, 0 h

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

characteristic: cell type

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Oct4, 0 h


E-MTAB-5342:Oct4, 24 h

text: public

text: E-MTAB-5342:Oct4, 24 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

characteristic: description

text: Esrrb-tet-on

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Oct4, 24 h


E-MTAB-5342:Oct4, 48 h

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-5342:Oct4, 48 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Oct4, 48 h


E-MTAB-5342:Oct4, 72 h

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5342:Oct4, 72 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Oct4, 72 h


E-MTAB-5342:Oct4, 8 h

text: public

text: E-MTAB-5342:Oct4, 8 h

characteristic: Submitter Id

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Oct4, 8 h

characteristic: title


E-MTAB-5342:Sox2, 0 h

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5342:Sox2, 0 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sox2, 0 h


E-MTAB-5342:Sox2, 24 h

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-5342:Sox2, 24 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sox2, 24 h


E-MTAB-5342:Sox2, 48 h

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5342:Sox2, 48 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sox2, 48 h


E-MTAB-5342:Sox2, 72 h

text: public

text: E-MTAB-5342:Sox2, 72 h

text: ArrayExpress

text: epiblast stem cell

text: house mouse

characteristic: common name

text: Esrrb-tet-on

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sox2, 72 h


E-MTAB-5342:Sox2, 8 h

text: public

text: E-MTAB-5342:Sox2, 8 h

text: ArrayExpress

characteristic: broker name

text: epiblast stem cell

characteristic: cell type

text: house mouse

text: Esrrb-tet-on

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sox2, 8 h


text: PASTEUR

text: public


text: Universitat Pompeu Fabra

text: public

tag: Namespace:Universitat Pompeu Fabra

text: human

text: Birhor

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Whole Genome Sequences of Indian Individual


characteristic: ENA-LAST-UPDATE

text: Universitat Pompeu Fabra

text: public

text: human

text: Uttarpradesh Brahmin

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Irula

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Bengali

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Punjabi

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Rajput

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Riang

text: Homo sapiens

text: Homo sapiens


text: Universitat Pompeu Fabra

text: public

text: human

text: Vellalar

text: Homo sapiens

text: Homo sapiens


text: female

characteristic: ArrayExpress-Sex

text: mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: wildtype preovulatory

characteristic: sample description

text: Mus musculus


text: female

text: mus musculus

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: heterozygous preovulatory

text: Mus musculus


text: female

text: mus musculus

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: KO preovulatory

text: Mus musculus

characteristic: title


text: female

text: mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: heterozygous 24h post hCG

text: Mus musculus


text: female

text: mus musculus

text: SC

text: public

characteristic: SRA accession

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: KO 24h post hCG

text: Mus musculus


text: female

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: heterozygous 32h post hCG

text: Mus musculus


text: female

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: wildtype 32h post hCG

text: Mus musculus


text: female

text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: KO 32h post hCG

text: Mus musculus


text: public

characteristic: description

text: metagenome

text: metagenome


characteristic: ENA-LAST-UPDATE

text: public

text: Bacterial rrs, amoA and nifH

text: metagenome

text: metagenome


text: PASTEUR

text: public


text: public

tag: Namespace:KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

characteristic: collection date

text: bulk soil

characteristic: environment (biome)

text: field

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: unidentified bacterium

characteristic: project name

text: unidentified bacterium

text: Illumina MiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Bulk soils to be compared to rhizosphere communities of the plant Saxifraga oppositifolia along a glacier chronosequence


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: bulk soil

text: field

text: soil

text: Norway

text: metagenome

text: unidentified bacterium

text: unidentified bacterium

text: Illumina MiSeq

text: soil

characteristic: title


E-MTAB-4214:Sample 1

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4214:Sample 1

tag: Namespace:BioISI - Biosystems, Integrative Sciences Institute Instituto de Medicina Molecular University of Lisbon

text: ArrayExpress

characteristic: broker name

text: CD4-positive helper T cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Human samples, cell isolation and TCR-stimulation Peripheral blood mononuclear cells (PBMC) were isolated from buffy coats of healthy individuals by Ficcol-Paque PLUS (GE Healthcare, Uppsala, Sweden) density gradient centrifugation. Subsequently, naïve CD4+ T cells were magnetically isolated by negative selection using the EasySep™ Human Naïve CD4+ T Cell Enrichment kit (Stem Cell Technologies), according to the manufacturer’s instructions, with purity was always above 97% as assessed by flow cytometry (CD45RA+CD45ROnegCD4+CD3+ cells). Isolated naive cells were cultured in complete culture medium: RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-glutamine, 100 U/ml penicillin -100μg/ml streptomicin, and 0,05mg/ml Gentamicin (all from Invitrogen). For TCR-stimulation, naïve CD4+ T cells were cultured for 72h at 2,5x106 cells/ml in complete culture medium in the presence of plate-bound anti-CD3 (1μg/ml, clone OKT3, eBioscience), soluble anti-CD28 (1μ/ml, clone 28.2, BD-Pharmingen) and 10IU/ml of IL-2 (Dr. Maurice Gately, Hoffmann-La Roche Inc, NIH AIDS Reagent Program). For prolongued time-course assays, cells were switched to medium supplemented with IL-2 after the initial 72h culture. Virus production and HIV infections 293T cells were transfected with pRod (NIBSC - Centre for AIDS Reagents, Medical Research Council UK) or pNL4-3 (NIH AIDS Reagent Program) for 24 hours using fuGENE HD Transfection Reagent (Roche), according to the manufacturer’s instructions. Cell-free culture supernatants were quantified in terms of reverse transcriptase (RT) activity using a Cavidi Lenti RT Activity Kit (Cavidi Tech AB, Uppsala, Sweden), according to manufacturer’s instructions. Viral stocks were concentrated by ultracentrifugation (30 minutes at 50,000g and 4ºC using a Beckmann L8-60M ultracentrifuge) before being resuspended in complete medium supplemented with polybrene (3µg/ml; Sigma) and used to infect primary cells or stably-transfected cell lines, at a dose of 0.853ng RT/106 cells. After an initial culture period of 3 hours under standard conditions (37ºC/5%CO2) cells were washed to remove residual virus. Infected unstimulated and TCR-stimulated naïve CD4+ T cells were resuspended in medium supplemented with 10IU/ml IL-2 and polybrene (3µg/ml), and cultured at 37ºC for a total of 24 hours. After this period, cells and supernatants were collected and stored immediately at -80ºC. HIV-1NL43 infected cell lines (JØ and J34c, see below) were cultured in complete medium supplemented with polybrene (3µg/ml) and 1µg/ml G418 (Life technologies) for a total of 48 hours. Culture supernatants and cell pellets were harvested at 24 and 48 hours. Infection was assessed by quantifying cell-associated viral DNA and gag and tat mRNA levels were quantified as described previously (Soares et al., 2011). Viral production was assessed by measuring RT activity in supernatants using SYBR green product-enhanced RT (SG-PERT) as previously described (Nunes-Cabaço et al., 2015). Total RNA from naïve CD4+ T cells was isolated using mirVana miRNA Isolation kit (Ambion) according to the manufacturer’s instructions. Trizol reagent (Ambion) was used for isolation of total RNA from Jurkat cells, according to the manufacturer’s instructions. RNA quantification was performed on a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). For small-RNA-seq and microarray analysis, the quality of total RNA was validated using a 2100 Bioanalyzer (Agilent Technologies), RNA 6000 Nano LabChip kits, and 2100 expert software for individual samples. Only samples without visible degradation in the Bioanalyzer profile were selected for further downstream analysis. Total RNA samples from multiple individuals were pooled for the generation of sequencing libraries (see below) and re-quantified using Qubit (Life technologies). Small RNA-Seq design and sequencing The small-RNA-seq libraries used in this study were generated in three distinct experiments by outsourcing. Total RNA samples were gel fractionated and fragments between 15 and 30bp were purified and used to generate small RNA-seq libraries according to Illumina’s Small RNA-seq protocol. Dataset 1 was generated in a pilot experiment in which total RNA samples were generated for each condition (naïve and activated CD4+ T-cells) by pooling equal amounts of total RNA obtained from 9 individuals to generate a single RNA pool per condition. Small-RNA-seq libraries derived from these samples were sequenced using the Genome Analyser II sequencer (Illumina), in separate lanes, occupying the whole flow cell using the Chrysalis 36 cycles v 4.0 sequencing kit. Dataset 2 was generated in a second experiment, in which equal amounts of total RNA obtained from three individuals were pooled in balanced sets of three, generating to two replicate RNA pools per condition (quiescent naïve, quiescent naïve infected with HIV-1 and quiescent naïve infected with HIV-2), from a total of six donnor. Dataset 3 was generated in a third experiment in which total RNA samples from 3 individuals were pooled per condition (stimulated naïve, stimulated naïve infected with HIV-1 and stimulated naïve infected with HIV-2) and three replicate libraries were generated from a total of 9 donnors. Libraries from the second and third experiments were sequenced using the HiSeq2000 sequencer (Illumina) using the TruSeq(TM) SBS v5 sequencing kit, occupying 20% of the lane. The same 3’ sequencing adaptor (ATCTCGTATGCCGTCTTCTGCTTGT) was used in all experiments allowing comparison of results and was removed from raw data before analysis. Raw sequencing data from dataset 1 was pre-processed using the SCS.2.6 and CASAVA.1.6 pipeline (Illumina). Raw reads from datasets 2 and 3 were pre-processed using the HiSeq Control Soft. V 1.3.8, RTA 1.10.36, CASAVA 1.7.0 and OLB-1.9.0 (Illumina).

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: naive T cell CD4+

characteristic: phenotype

text: Homo sapiens

text: Sample 1


E-MTAB-4214:Sample 10

characteristic: ENA-CHECKLIST

text: BioISI - Biosystems, Integrative Sciences Institute Instituto de Medicina Molecular University of Lisbon

text: public

text: E-MTAB-4214:Sample 10

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 10


E-MTAB-4214:Sample 11

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4214:Sample 11

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 11


E-MTAB-4214:Sample 12

characteristic: External Id

text: public

text: E-MTAB-4214:Sample 12

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 12


E-MTAB-4214:Sample 13

characteristic: INSDC center name

text: public

text: E-MTAB-4214:Sample 13

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 13


E-MTAB-4214:Sample 14

characteristic: INSDC first public

text: public

text: E-MTAB-4214:Sample 14

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 14


E-MTAB-4214:Sample 15

characteristic: INSDC last update

text: public

text: E-MTAB-4214:Sample 15

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 15


E-MTAB-4214:Sample 16

text: public

characteristic: INSDC status

text: E-MTAB-4214:Sample 16

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 16


E-MTAB-4214:Sample 17

text: public

characteristic: SRA accession

text: E-MTAB-4214:Sample 17

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 17


E-MTAB-4214:Sample 2

text: public

text: E-MTAB-4214:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 2


E-MTAB-4214:Sample 3

text: public

text: E-MTAB-4214:Sample 3

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: naive T cell CD4+

text: Homo sapiens

text: Sample 3

characteristic: title


E-MTAB-4214:Sample 4

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4214:Sample 4

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 4


E-MTAB-4214:Sample 5

text: public

text: E-MTAB-4214:Sample 5

text: ArrayExpress

characteristic: broker name

text: CD4-positive helper T cell

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 5


E-MTAB-4214:Sample 6

text: public

text: E-MTAB-4214:Sample 6

text: ArrayExpress

text: CD4-positive helper T cell

characteristic: cell type

text: human

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 6


E-MTAB-4214:Sample 7

text: public

text: E-MTAB-4214:Sample 7

text: ArrayExpress

text: CD4-positive helper T cell

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 7


E-MTAB-4214:Sample 8

text: public

text: E-MTAB-4214:Sample 8

text: ArrayExpress

text: CD4-positive helper T cell

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 8


E-MTAB-4214:Sample 9

text: public

text: E-MTAB-4214:Sample 9

text: ArrayExpress

text: CD4-positive helper T cell

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: stimulated-naive T cell CD4+

text: Homo sapiens

text: Sample 9


E-MTAB-43671481641089:MO7EKI ERG a

text: public

text: E-MTAB-43671481641089:MO7EKI ERG a

tag: Namespace:INSERM U1170, Equipe Labellisee Ligue Contre le Cancer, Villejuif, France Institut Gustave Roussy, Villejuif, France  Universite Paris Diderot, Paris, France

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: The human MO7e and MO7e-KI AMKL cell lines were cultured in MEM-α supplemented with 20% FBS, Penicillin (100U/mL)-Streptomycin (100µg/mL) and 2mM L-Glutamine (Gibco), and 5 ng/ml of human GM-CSF (PeproTech). HEL cells are cultured in RPMI1640 supplemented with 10% FBS, Penicillin (100U/mL)-Streptomycin (100µg/mL), 2mM L-Glutamine (Gibco). AMKL cells obtained directly from immunodeficient animals or after purification by flow cytometry were cultured in RPMI 1640 medium supplemented with 20% FBS, Penicillin (100U/mL)-Streptomycin (100µg/mL) and 2mM L-Glutamine (Gibco), and 10 ng/ml each of human SCF, IL3, IL6, IL11, TPO, 10U/ml EPO and 5 ng/ml of GM-CSF (PeproTech). ChIP protocol was adapted from the MagnaChIP kit protocol (Millipore). Cells (AMKL and MO7e-KI) were fixed with 1% formaldehyde, lysed with Cell Lysis and then Nuclear Lysis buffers respecting concentration of 20.106 cells per mL, and finally sonicated (30-min cycle on Covaris apparatus; KBioscience). Sheared chromatin was immunoprecipitated overnight using the following antibodies: anti-CBFA2T3 (Abcam, ab33072), anti-ERG (Santa Cruz ; SC354), anti-GATA3 (Santa Cruz ; mix 50/50 of SC268X and SC269X), anti-H3K27ac (ActiveMotif, #39133), anti-H3K4me1 (Diagenode ; #C15410037), anti-H3K4me3 (Diagenode, #C15410003), anti-H3K27me3 (Cell Signaling, #9733S) and rabbit IgG (Upstate, #12-370). 1/10 of the sheared chromatin was used as a reference (Input). Immune complex collection was realized with Protein G Sepharose (Sigma-Aldrich; P3296), 1h30 at +4°C. For GFP-ChIP, GFP-Trap agarose beads were used (Chromotek). Rinses were done according to MagnaChIP kit protocol with Low salt, High salt and LiCL immune complex wash buffers. Finally, elution was realized according the IPure Kit protocol (Diagenode, Cat No C03010012) following manufacturer’s instructions. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an 'A' base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bioo Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter) and amplified by PCR for 10 cycles more.

text: acute megakaryoblastic leukaemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI ERG a


E-MTAB-43671481641089:MO7EKI ERG b

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSERM U1170, Equipe Labellisee Ligue Contre le Cancer, Villejuif, France Institut Gustave Roussy, Villejuif, France Universite Paris Diderot, Paris, France

text: public

text: E-MTAB-43671481641089:MO7EKI ERG b

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI ERG b


E-MTAB-43671481641089:MO7EKI ETO2 a

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-43671481641089:MO7EKI ETO2 a

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI ETO2 a


E-MTAB-43671481641089:MO7EKI ETO2 b

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-43671481641089:MO7EKI ETO2 b

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI ETO2 b


E-MTAB-43671481641089:MO7EKI GFP a

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-43671481641089:MO7EKI GFP a

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI GFP a


E-MTAB-43671481641089:MO7EKI H3K27ac a

text: public

text: E-MTAB-43671481641089:MO7EKI H3K27ac a

characteristic: Submitter Id

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI H3K27ac a

characteristic: title


E-MTAB-43671481641089:MO7EKI H3K27ac b

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-43671481641089:MO7EKI H3K27ac b

text: ArrayExpress

characteristic: broker name

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI H3K27ac b


E-MTAB-43671481641089:MO7EKI H3K27me3 a

text: public

text: E-MTAB-43671481641089:MO7EKI H3K27me3 a

text: ArrayExpress

text: human

characteristic: common name

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI H3K27me3 a


E-MTAB-43671481641089:MO7EKI H3K4me3 a

text: public

text: E-MTAB-43671481641089:MO7EKI H3K4me3 a

text: ArrayExpress

text: human

characteristic: description

text: acute megakaryoblastic leukaemia

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: MO7EKI H3K4me3 a


E-MTAB-43671481641089:MO7EKI H3K4me3 b

text: public

text: E-MTAB-43671481641089:MO7EKI H3K4me3 b

text: ArrayExpress

text: human

text: acute megakaryoblastic leukaemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: MO7EKI H3K4me3 b


text: Alfred Wegener Institute

text: public

tag: Namespace:Alfred Wegener Institute

text: Sporophytes of D. anceps Montagne were raised from gametophyte cultures which were established from spores of fertile sporophytes collected at Potter Cove (King George Island; South Shetland Islands, Antarctica 62°14’S-58°38’W, AWI culture numbers: 3064, 3084)

characteristic: culture collection

text: young sporophytes

characteristic: dev stage

text: Antarctica

characteristic: geographic location (country and/or sea)

text: Potter Cove

characteristic: geographic location (region and locality)

characteristic: lat lon

text: Desmarestia anceps

text: Desmarestia anceps

text: Desmarestia anceps RNA-Seq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: PASTEUR

characteristic: INSDC center name

text: public

text: Salmonella enterica subsp. enterica serovar Enteritidis


CECT 9026

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CECT 9026

characteristic: collection date

text: estuary Odiel river, Huelva

characteristic: environment (biome)

text: estuary

characteristic: environment (feature)

text: plant root

characteristic: environment (material)

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Vibrio sp. CECT 9026

text: plant-associated

characteristic: plant-associated environmental package

text: Whole genome sequencing of Vibrio spartinae CECT 9026, type strain

characteristic: project name

text: Vibrio sp. CECT 9026

text: Illumina Miseq

characteristic: sequencing method

text: CECT 9026T

characteristic: strain

text: Vibrio spartinae CECT 9026T


CECT 9027

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

text: public

text: CECT 9027

characteristic: Submitter Id

text: estuary Odiel river, Huelva

text: estuary

text: Arthrocnemum machrostachyum leaves

text: Spain

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: Vibrio sp. CECT 9027

characteristic: organism

text: plant-associated

text: Whole genome sequencing of Vibrio palustris CECT 9027, type strain

text: Vibrio sp. CECT 9027

text: Illumina Miseq

text: CECT 9027T

text: Vibrio palustris CECT 9027T

characteristic: title