characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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

characteristic: Submitter Id

characteristic: bacteria count (cells / ml)

characteristic: collection date

characteristic: ctd cast no.

text: Dispersal-transplant experiment

characteristic: doc (micro-molar / ml)

text: microorganisms

text: estuary

text: water

text: NO

text: Bakt_341F (CCTACGGGNGGCWGCAG)

text: Canada

text: St. Lawrence estuary

text: IOW

text: metagenome

text: RNA

characteristic: nh4+ (micro-molar / ml)

characteristic: no2- (micro-molar / ml)

characteristic: no3- (micro-molar / ml)

text: organismal metagenomes

characteristic: po43- (micro-molar / ml)

text: MicroFun (DFG)

characteristic: project name

characteristic: protist count (cells / ml)

text: Dandan Shen

characteristic: responsible researcher

text: Bakt_805R (GACTACHVGGGTATCTAATCC)

characteristic: reverse primer

characteristic: salinity (psu)

text: organismal metagenomes

text: 16 S amplicon Illumina Miseq

characteristic: sequencing method

characteristic: sio2- (micro-molar / ml)

text: > 0.2 micro-meter

characteristic: size fraction

text: microcosms

characteristic: study type

characteristic: temperature (degrees centigrade)

text: GSC MIxS water

characteristic: water environmental pacakge

text: water

characteristic: water environmental package

text: CTD instrument

characteristic: water sample collection device


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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

tag: Namespace:IOW - Leibniz Institute for Baltic Sea Research

characteristic: Submitter Id

characteristic: bacteria count (cells / ml)

characteristic: collection date

characteristic: ctd cast no.

text: Dispersal-transplant experiment

characteristic: description

text: microorganisms

characteristic: environment (biome)

text: estuary

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: NO

characteristic: fixative for rna prep

text: Bakt_341F (CCTACGGGNGGCWGCAG)

characteristic: forward primer

text: Canada

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: St. Lawrence estuary

characteristic: geolocation name

text: IOW

characteristic: insitution

text: metagenome

characteristic: investigation type

text: RNA

characteristic: molecule

text: organismal metagenomes

characteristic: organism

text: MicroFun (DFG)

text: Dandan Shen

text: Bakt_805R (GACTACHVGGGTATCTAATCC)

text: organismal metagenomes

text: 16 S amplicon Illumina Miseq

text: > 0.2 micro-meter

text: microcosms

characteristic: title

text: GSC MIxS water

text: water

text: CTD instrument

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IOW - Leibniz Institute for Baltic Sea Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: bacteria count (cells / ml)

characteristic: collection date

characteristic: ctd cast no.

text: Dispersal-transplant experiment

text: microorganisms

text: estuary

text: water

text: NO

text: Bakt_341F (CCTACGGGNGGCWGCAG)

text: Canada

text: St. Lawrence estuary

text: IOW

text: metagenome

text: RNA

text: organismal metagenomes

text: MicroFun (DFG)

characteristic: project name

characteristic: protist count (cells / ml)

text: Dandan Shen

characteristic: responsible researcher

text: Bakt_805R (GACTACHVGGGTATCTAATCC)

characteristic: reverse primer

text: organismal metagenomes

text: 16 S amplicon Illumina Miseq

characteristic: sequencing method

text: > 0.2 micro-meter

characteristic: size fraction

text: microcosms

characteristic: study type

characteristic: temperature (degrees centigrade)

text: GSC MIxS water

characteristic: water environmental pacakge

text: water

characteristic: water environmental package

text: CTD instrument

characteristic: water sample collection device


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HEINRICH HEINE UNIVERSITY DUESSELDORF

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:HEINRICH HEINE UNIVERSITY DUESSELDORF

text: oomycete associated with Malus domestica

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: uncultured Oomycetes

characteristic: organism

text: plant-associated

characteristic: plant-associated environmental package

text: Protistbiome

text: uncultured Oomycetes

text: Illumina

text: Protistbiome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: HEINRICH HEINE UNIVERSITY DUESSELDORF

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: terrestrial biome

text: organic feature

text: root

text: Germany

text: metagenome

text: uncultured Oomycetes

text: plant-associated

text: Protistbiome

characteristic: project name

text: uncultured Oomycetes

text: Illumina

characteristic: sequencing method

text: Protistbiome


Mock

characteristic: External Id

text: HEINRICH HEINE UNIVERSITY DUESSELDORF

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Mock

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: culture

text: Germany

text: metagenome

text: uncultured Oomycetes

text: plant-associated

text: Protistbiome

text: uncultured Oomycetes

text: Illumina

text: Protistbiome


text: Schistosoma mansoni

characteristic: ArrayExpress-Species

text: Puerto Rican strain NMRI

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Schistosoma mansoni

characteristic: common name

text: Schistosoma mansoni

characteristic: organism

text: Cell populations isolated by FACS from adult worms, RNA used to make amplified cDNA libraries

characteristic: sample description

text: Schistosoma mansoni

text: Puerto Rican strain NMRI

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LIMM

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: metagenome

text: metagenome

text: IBD IBS microbiome


characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: control

characteristic: infection

characteristic: latitude

text: adult

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: colon

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: colon

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:small intestine

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: control

text: adult

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: small intestine

text: mouse gut metagenome

text: female

text: small intestine

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:colon

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: control

characteristic: infection

characteristic: latitude

text: adult

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: colon

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: colon

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: control

text: adult

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: male

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: control

characteristic: infection

characteristic: latitude

text: adult

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: infected

text: adult

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: female

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: infected

characteristic: infection

characteristic: latitude

text: adult

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: infected

text: adult

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: male

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: infected

characteristic: infection

characteristic: latitude

text: adult

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: control

text: neonate

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: male

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: control

characteristic: infection

characteristic: latitude

text: neonate

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: control

text: neonate

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: female

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: control

characteristic: infection

characteristic: latitude

text: neonate

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: infected

text: neonate

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: female

text: colon

characteristic: title

text: Giardia infection early life

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:small intestine

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: infected

characteristic: infection

characteristic: latitude

text: neonate

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: small intestine

characteristic: sample type

text: mouse gut metagenome

text: female

characteristic: sex

text: small intestine

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:colon

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: infected

text: neonate

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: colon

text: mouse gut metagenome

text: female

text: colon

text: Giardia infection early life

characteristic: title

text: grams


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: Missing: Not provided

text: weeks

text: UBERON:gastrointestinal system

text: UBERON:lumen of gut

text: UBERON:colon

text: TRUE

text: urban biome

text: animal-associated habitat

characteristic: env feature

text: host-associated

characteristic: env package

text: intestine environment

text: Germany:Aachen

characteristic: geo loc name

text: mouse

characteristic: host common name

text: Mus musculus

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: infected

characteristic: infection

characteristic: latitude

text: neonate

characteristic: life stage

characteristic: litter

characteristic: longitude

text: mouse gut metagenome

text: RWTH Aachen

text: FALSE

text: colon

characteristic: sample type

text: mouse gut metagenome

text: male

characteristic: sex

text: colon

characteristic: tissue

text: Giardia infection early life

characteristic: weight

text: grams


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

characteristic: Submitter Id

text: Missing: Not provided

characteristic: age

text: weeks

characteristic: age units

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:lumen of gut

characteristic: body product

text: UBERON:small intestine

characteristic: body site

characteristic: description

text: TRUE

characteristic: elevation

text: urban biome

characteristic: env biome

text: animal-associated habitat

text: host-associated

text: intestine environment

text: Germany:Aachen

text: mouse

text: Mus musculus

text: infected

text: neonate

text: mouse gut metagenome

characteristic: organism

text: RWTH Aachen

text: FALSE

text: small intestine

text: mouse gut metagenome

text: male

text: small intestine

characteristic: title

text: Giardia infection early life

text: grams


WMS RM15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: WMS RM15

tag: Namespace:Computational Biology and Microbial Ecology

characteristic: collection date

text: Whole metagenomic sequencing of superficial water sample from the Bogotá River

text: area of developed open space

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

text: Anthropic Effects on Aquatic Microbial Communities and Antibiotic Resistance Genes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: WMS River Middle Section 2015

text: water

characteristic: water environmental package


WMS RM16

text: Computational Biology and Microbial Ecology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: WMS RM16

characteristic: Submitter Id

characteristic: description

text: area of developed open space

text: river

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: WMS River Middle Section 2016

characteristic: title

text: water


16S RM15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 16S RM15

characteristic: collection date

text: 16S rRNA gene amplicon sequencing of superficial water sample from the Bogotá River

text: area of developed open space

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: 16S River Middle Section 2015

text: water


16S RM16

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 16S RM16

text: area of developed open space

text: river

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: 16S River Middle Section 2016

text: water

characteristic: water environmental package


WMS RS16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: WMS RS16

characteristic: Submitter Id

characteristic: description

text: alpine paramo

text: river

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: WMS River Source 2016

characteristic: title

text: water


16S RS16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 16S RS16

characteristic: collection date

text: alpine paramo

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: 16S River Source 2016

text: water


WMS RL15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: WMS RL15

text: area of developed space with high usage intensity

text: river

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: WMS River Lower Section 2015

text: water

characteristic: water environmental package


WMS RL16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: WMS RL16

characteristic: Submitter Id

characteristic: description

text: river

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: WMS River Lower Section 2016

characteristic: title

text: water


16S RL15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 16S RL15

characteristic: collection date

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: 16S River Lower Section 2015

text: water


16S RL16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 16S RL16

text: river

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: 16S River Lower Section 2016

text: water

characteristic: water environmental package


WMS HA15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: WMS HA15

characteristic: Submitter Id

text: Whole metagenomic sequencing of superficial water sample from hospital wastewaters

characteristic: description

text: wastewater

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: WMS Hospital A wastewater 2015

characteristic: title

text: water


WMS HB15

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: WMS HB15

characteristic: collection date

characteristic: environment (biome)

text: wastewater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: WMS Hospital B wastewater 2015

text: water


WMS HC15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: WMS HC15

text: wastewater

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: WMS Hospital C wastewater 2015

text: water

characteristic: water environmental package


WMS HA16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: WMS HA16

characteristic: Submitter Id

characteristic: description

text: wastewater

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: WMS Hospital A wastewater 2016

characteristic: title

text: water


WMS HB16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: WMS HB16

characteristic: collection date

characteristic: environment (biome)

text: wastewater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: WMS Hospital B wastewater 2016

text: water


WMS HC16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: WMS HC16

text: wastewater

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: WMS Hospital C wastewater 2016

text: water

characteristic: water environmental package


16S HA15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 16S HA15

characteristic: Submitter Id

text: 16S rRNA gene sequencing of superficial water sample from hospital wastewaters

characteristic: description

text: wastewater

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: 16S Hospital A wastewater 2015

characteristic: title

text: water


16S HB15

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 16S HB15

characteristic: collection date

characteristic: environment (biome)

text: wastewater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: 16S Hospital B wastewater 2015

text: water


16S HC15

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: 16S HC15

text: wastewater

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: 16S Hospital C wastewater 2015

text: water

characteristic: water environmental package


16S HA16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 16S HA16

characteristic: Submitter Id

characteristic: description

text: wastewater

text: water

text: Colombia

text: metagenome

text: metagenomes

characteristic: organism

text: metagenomes

text: Illumina

text: 16S Hospital A wastewater 2016

characteristic: title

text: water


16S HB16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 16S HB16

characteristic: collection date

characteristic: environment (biome)

text: wastewater

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Colombia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenomes

text: metagenomes

text: Illumina

text: 16S Hospital B wastewater 2016

text: water


16S HC16

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 16S HC16

text: wastewater

text: water

text: Colombia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

characteristic: project name

text: metagenomes

text: Illumina

characteristic: sequencing method

text: 16S Hospital C wastewater 2016

text: water

characteristic: water environmental package


CTH-K

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CSIRO

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CTH-K

characteristic: Submitter Id

text: bread wheat

characteristic: common name

text: Canthatch

characteristic: cultivar

text: Triticum aestivum

characteristic: host scientific name

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: PE reads from flow-sorted chr7D

characteristic: title


CTH-W

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CSIRO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: CTH-W

text: bread wheat

text: Canthatch

text: Triticum aestivum

text: Triticum aestivum

text: Triticum aestivum

text: PE reads from flow-sorted chr7D


text: CSIRO

text: public

text: bread wheat

text: Canthatch

text: Triticum aestivum

text: Triticum aestivum

text: Triticum aestivum

text: PE reads from flow-sorted chr7D


Canthatch-K

text: CSIRO

text: public

text: Canthatch-K

text: bread wheat

text: Canthatch

text: un-anchored, repeat masked (TREP rel16) contigs of chr7D enriched sequences

characteristic: description

text: Triticum aestivum

text: Triticum aestivum

text: Assembled reads from flow-sorted chr7D


Canthatch-W

text: CSIRO

text: public

text: Canthatch-W

text: bread wheat

text: Canthatch

text: Triticum aestivum

text: Triticum aestivum

text: Assembled reads from flow-sorted chr7D


text: UNIVERSITY OF OSLO

text: public

tag: Namespace:UNIVERSITY OF OSLO

text: Italian sparrow

text: bam-file with whole genome resequencing data

text: Crete

characteristic: geographic location (region and locality)

text: Passer italiae

text: Passer italiae

text: Male

characteristic: sex

text: Blood

characteristic: tissue type

text: ItalianIslandSparrow


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF OSLO

characteristic: INSDC last update

text: public

text: Italian sparrow

text: Crete

text: Passer italiae

text: Passer italiae

text: Male

text: Blood

text: ItalianIslandSparrow


text: UNIVERSITY OF OSLO

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Italian sparrow

text: Sicily

text: Passer italiae

text: Passer italiae

text: Male

text: Blood

text: ItalianIslandSparrow


text: UNIVERSITY OF OSLO

text: public

text: Italian sparrow

characteristic: common name

text: Malta

text: Passer italiae

text: Passer italiae

text: Male

text: Blood

text: ItalianIslandSparrow


text: UNIVERSITY OF OSLO

text: public

text: Italian sparrow

text: Corsica

text: Passer italiae

characteristic: organism

text: Passer italiae

text: Male

text: Blood

text: ItalianIslandSparrow


text: SSI

text: public

text: SSI

characteristic: collected by

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: Homo sapiens

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Typhimurium

characteristic: serovar

text: Salmonella isolates positive for mcr-3

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SSI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SSI

text: No

text: Denmark

text: not provided

text: Homo sapiens

text: Yes

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: O:4,5,12; H:i:-

text: Salmonella isolates positive for mcr-3


text: SSI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SSI

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: Yes

text: Salmonella enterica subsp. enterica

characteristic: organism

text: Salmonella enterica subsp. enterica

text: O:4,12; H:i:-

text: Salmonella isolates positive for mcr-3


text: University of Edinburgh

text: public

tag: Namespace:University of Edinburgh

text: Unheated glass house

characteristic: air temperature regimen

characteristic: estimated size

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: glasshouse

characteristic: growth facility

text: reference not yet available; collected from the wild, and potted in standard mix and kept in glasshouse at University of Edinburgh; no controlled lighting or heating; publication title: “Maintaining their genetic distance: little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems”

characteristic: isolation and growth condition

text: Glasshouse with no supplemental lighting

characteristic: light regimen

characteristic: number of replicons

text: Geum urbanum

text: after true leaves formed, pre-flower production

characteristic: plant developmental stage

text: Standard low-peat potting mix

characteristic: plant growth medium

text: young leaf

characteristic: plant structure

text: hexaploid

characteristic: ploidy

text: asexual

characteristic: propagation

text: 10-inch diameter pot

characteristic: rooting conditions

text: healthy

characteristic: sample health state

text: Geum urbanum

text: G. urbanum draft genome sample

text: Light watering daily;l species prefers drier soil

characteristic: watering regimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CEA CADARACHE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CEA CADARACHE

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: testtest

characteristic: title


text: CEA CADARACHE

text: public

text: Abbott's mouse

text: Mus abbotti

text: Mus abbotti

text: todeltodel


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: public

tag: Namespace:Institut de recherche experimentale et clinique - IREC

text: Samir Fakhour

characteristic: collected by

characteristic: collection date

text: Morocco

characteristic: geographic location (country and/or sea)

text: Samir Fakhour

characteristic: identified by

text: Sitobion avenae, Rhopalosiphum padi, R. maidis, Sipha maydis and Diuraphis noxia

characteristic: lab host

text: Aphididae gen. sp. SS-2008

text: Aphididae gen. sp. SS-2008

text: A large-scale field study of bacterial communities in cereal aphid across Morocco


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut de recherche experimentale et clinique - IREC

text: public

text: Samir Fakhour

text: Morocco

text: Samir Fakhour

text: Aphididae gen. sp. SS-2008

text: Aphididae gen. sp. SS-2008


text: ZMBH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: Norway rat

text: Protocols: Blood collected from infected or uninfected (control) rats into Paxgene tubes Rats were infected IP with Trypanosoma brucei rhodesiense Parasitaemias were counted in diluted blood using a haemocytometer just before blood collection. Standard Paxgene protocol on whole blood Ribo-Globin then by Illumina TruSeq Total Stranded RNA preparation kit (Illumina, RS-122-2301)

characteristic: description

text: Rattus norvegicus

text: Rattus norvegicus

text: blood

characteristic: organism part

text: Rattus norvegicus

unit: unit per milliliter

characteristic: trypanosomes measurement


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Cells were grown in M9 minimal medium supplemented with 0.4 % glucose to 801 exponential phase (0.2 OD 650 nm). Study of the mechanisms of RecB mutant terminus DNA loss in Escherichia coli. FX158: WT MG1655 FX35: recB- FX37: ruvAB- FX51: matP- MIC18: recB- sbcD- sbcC- MIC20: recB- ruvAB- MIC24: matP- recB- MIC25: recA- recB- MIC31: sbcB- sbcD- MIC34: recA- recD- MIC40: linear chromosome MIC41: linear chromosome recB- MIC42: matP- ftsKC- MIC43: matP- ftsKC- recB- MIC48: recA- Cells were grown in M9 minimal medium supplemented with 0.4 % glucose to exponential phase (0.2 OD 650 nm). Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. Genomic DNA Libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina). Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies).

text: linear chromosome

characteristic: genotype

characteristic: growth condition

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

characteristic: organism

text: linear

characteristic: title


E-MTAB-6122:linear recB

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6122:linear recB

text: ArrayExpress

text: linear chromosome, recB

text: M9 minimal medium supplemented with 0.4 % glucose

text: linear recB


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: matP

text: matP


E-MTAB-6122:matP FtsKdc

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6122:matP FtsKdc

text: ArrayExpress

text: matP FtsKCter

text: matP FtsKdc


E-MTAB-6122:matP FtsKdc recB

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-6122:matP FtsKdc recB

text: ArrayExpress

text: matP FtsKCter recB

text: matP FtsKdc recB


E-MTAB-6122:matP recB

text: public

text: E-MTAB-6122:matP recB

text: ArrayExpress

characteristic: broker name

characteristic: description

text: matP recB

text: matP recB


text: public

text: ArrayExpress

text: recA

text: recA


E-MTAB-6122:recA recB

text: public

text: E-MTAB-6122:recA recB

text: ArrayExpress

text: recA recB

text: recA recB


E-MTAB-6122:recA recD

text: public

text: E-MTAB-6122:recA recD

text: ArrayExpress

text: recA recD

text: recA recD


text: public

text: ArrayExpress

text: recB

text: recB


text: public

text: ArrayExpress

text: ruvA ruvB

text: ruvAB


E-MTAB-6122:ruvAB recB

text: public

text: E-MTAB-6122:ruvAB recB

text: ArrayExpress

text: ruvA ruvB recB

text: ruvAB recB


E-MTAB-6122:sbcB sbcD

text: public

text: E-MTAB-6122:sbcB sbcD

text: ArrayExpress

text: sbcB sbcD

text: sbcB sbcD


E-MTAB-6122:sbcB sbcD recB

text: public

text: E-MTAB-6122:sbcB sbcD recB

text: ArrayExpress

text: sbcB sbcD recB

text: sbcB sbcD recB


text: public

text: ArrayExpress

text: wild type genotype

text: wt


text: Maynooth University

text: public

tag: Namespace:Maynooth University

text: bearded pig

characteristic: common name

text: 007 sequences

text: sus

characteristic: host scientific name

text: Ireland

characteristic: isolation source

text: Sus barbatus

text: Sus barbatus


text: Yeast

characteristic: ArrayExpress-PHENOTYPE

text: Saccharomyces cerevisiae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: baker's yeast

text: Saccharomyces cerevisiae

text: Yeast

characteristic: phenotype

text: Saccharomyces cerevisiae

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ETHZ

text: public

text: Adipocytes

characteristic: cell type

text: human

text: deep neck BAT

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


characteristic: External Id

text: ETHZ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Adipocytes

text: human

text: subcutaneous WAT

text: Homo sapiens

text: Homo sapiens


text: ETHZ

text: public

text: hMADS cells

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

tag: Namespace:Wellcome Trust Sanger Institute

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

text: house mouse

text: Protocols: Total RNA was purified by RNeasy Minikit (Qiagen) according to the manufacturer’s manual. RNA concentration was determined by Nanodrop, and 500 ng of total RNA was used for library construction using KAPA Stranded mRNA-Seq Kits. Sequencing was performed on Illumina HiSeq 2500 machines with 125 bp pair-end mode. The Dpf2 targeting vector was linearized and electroporated into R26::CreERT2 E14 cells to generate heterozygous ES cell lines after G418 selection. The selected heterozygous ES lines were transiently transfected with a FLP recombinase encoding plasmid (pCAGGsFlpE), converting the initial knockout allele (Dpf2+/-, lacZ positive, G418 resistant) into a “wild-type” (WT) allele with two floxP sites flanking exon 4 (Dpf2+/+, reverted WT (rWT), lacZ negative, G418 sensitive). Multiple independent rWT ES clones were then electroporated with the original Dpf2 knockout vector or Dpf2 critical exon-deleted targeting vector and selected with G418. Dpf2 critical-exon-deleted vector was generated by transforming Dpf2 targeting vector into the cre-containing bacteria. In the second round targeting, the clones recovered were only those with the second WT allele being targeted, which were confirmed by the presence of both the rWT allele and the second knockout allele. The long-range PCR reactions were carried out for genotyping (SequalPrep Long PCR kit, Invitrogen). The selected heterogeneous ES cell lines were converted to the conditional Dpf2+/+ and Dpf2+/- clones by transiently transfected with FlpE. RNeasy Minikit (Qiagen) KAPA Stranded mRNA-Seq Kits

text: normal

characteristic: disease

text: Dpf2 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wellcome Trust Sanger Institute

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: Total RNA was purified by RNeasy Minikit (Qiagen) according to the manufacturer’s manual. RNA concentration was determined by Nanodrop, and 500 ng of total RNA was used for library construction using KAPA Stranded mRNA-Seq Kits. Sequencing was performed on Illumina HiSeq 2500 machines with 125 bp pair-end mode. RNeasy Minikit (Qiagen) KAPA Stranded mRNA-Seq Kits

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus


characteristic: External Id

text: ROBERT KOCH INSTITUT

text: public

tag: Namespace:ROBERT KOCH INSTITUT

characteristic: collection date

text: sooty mangabey

text: fecal sample

text: Tropical rain forest primate gut

characteristic: environment (biome)

text: Gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Cote d'Ivoire

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Cercocebus atys

characteristic: organism

text: Hunting captures more than prey: evidence for microbiome assimilation by chimpanzees

characteristic: project name

text: Cercocebus atys

text: Illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ROBERT KOCH INSTITUT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Diana monkey

characteristic: common name

text: fecal sample

characteristic: description

text: Tropical rain forest primate gut

text: Gut

text: feces

text: Cote d'Ivoire

text: host-associated

text: mimarks-survey

text: Cercopithecus diana

text: Cercopithecus diana

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH INSTITUT

text: public

characteristic: Submitter Id

characteristic: collection date

text: Campbell's monkey

text: fecal sample

text: Tropical rain forest primate gut

characteristic: environment (biome)

text: Gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Cote d'Ivoire

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: host-associated

text: mimarks-survey

text: Cercopithecus campbelli

text: Cercopithecus campbelli

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ROBERT KOCH INSTITUT

text: public

text: lesser white-nosed monkey

text: fecal sample

text: Tropical rain forest primate gut

text: Gut

text: feces

text: Cote d'Ivoire

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Cercopithecus petaurista

characteristic: organism

characteristic: project name

text: Cercopithecus petaurista

text: Illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH INSTITUT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: king colobus

characteristic: common name

text: fecal sample

characteristic: description

text: Tropical rain forest primate gut

text: Gut

text: feces

text: Cote d'Ivoire

text: host-associated

text: mimarks-survey

text: Colobus polykomos

text: Colobus polykomos

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ROBERT KOCH INSTITUT

text: public

characteristic: Submitter Id

characteristic: collection date

text: fecal sample

text: Tropical rain forest primate gut

characteristic: environment (biome)

text: Gut

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Cote d'Ivoire

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: host-associated

text: mimarks-survey

text: Pan troglodytes verus

text: Pan troglodytes verus

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROBERT KOCH INSTITUT

text: public

text: white-nosed guenon

text: fecal sample

text: Tropical rain forest primate gut

text: Gut

text: feces

text: Cote d'Ivoire

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Cercopithecus nictitans

characteristic: organism

characteristic: project name

text: Cercopithecus nictitans

text: Illumina

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DTU Bioinformatics

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:DTU Bioinformatics

text: Eliava Institute

characteristic: collected by

text: PYO cocktail 1997 and 2014. Draft genomes

characteristic: description

text: Georgia

text: uncultured virus

text: uncultured virus

text: PYO cocktail


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU Bioinformatics

text: public

text: PYO2014_27_42.21.133.90.116.20.14.109.73

characteristic: Submitter Id

text: Eliava Institute

text: Georgia

characteristic: geographic location (country and/or sea)

text: uncultured virus

text: uncultured virus

text: PYO cocktail


text: DTU Bioinformatics

text: public

text: PYO97_10_85.139.47.48.59.38.5.35.15.78.55.44.14

text: Eliava Institute

text: Georgia

text: uncultured virus

characteristic: organism

text: uncultured virus

text: PYO cocktail


text: public

tag: Namespace:Department of Clinical Research, University of Bern, Switzerland.

text: ArrayExpress

characteristic: broker name

text: T-helper 1 cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Human CD4+ T cells were isolated from PBMC by EasySep positive selection kit (Stemcell Technologies) according to the manufacturer’s instructions. Positively selected CD4+ T cells were stained for subsequent TH cell subset sorting. Total RNA was isolated from TH1, TH2, TH17, and TH9 clones in the resting state with RNAready-kit (AmpTec) according to manufacturer’s instruction. Peripheral Blood Mononuclear Cells (PBMC) were isolated by Ficoll-Plaque Plus (GE Healthcare, UK) density gradient centrifugation. Culture medium consisted of PRMI-1640 with Hepes (GIBCO) supplemented with 5% of heat-inactivated human serum (Swiss Red Cross, Basel, Switzerland), 2mM L-Glutamine (Biochrom), 50U/ml penicillin and 50μg/ml streptomycin (Bioconcept) and 50 IU/ml IL-2 (Roche). T cells were cultured at a density of 0.25-1x105cells/96 well plate in a total volume of 200μL cell culture medium. Illumina TruSeq Stranded mRNA protocol Illumina TruSeq Stranded mRNA protocol

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: clonal culture

characteristic: growth condition

text: B

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: CXCR3+ CCR8- CCR6- CCR4-

characteristic: phenotype

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Department of Clinical Research, University of Bern, Switzerland.

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: T-helper 1 cell

text: human

text: normal

text: wild type genotype

text: clonal culture

text: B

text: Homo sapiens

text: Homo sapiens

text: blood

text: CXCR3+ CCR8- CCR6- CCR4-

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: T-helper 2 cell

text: human

characteristic: description

text: normal

text: wild type genotype

text: clonal culture

text: K

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: CXCR3- CCR8- CCR6- CCR4+

text: Homo sapiens


text: public

text: ArrayExpress

text: T-helper 2 cell

characteristic: cell type

text: human

characteristic: common name

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: clonal culture

characteristic: growth condition

text: L

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: CXCR3- CCR8- CCR6- CCR4+

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: T-helper 2 cell

text: human

text: normal

text: wild type genotype

text: clonal culture

text: N

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: CXCR3- CCR8- CCR6- CCR4+

characteristic: phenotype

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: T-helper 9 cell

text: human

text: normal

text: wild type genotype

text: clonal culture

text: C

text: Homo sapiens

text: Homo sapiens

text: blood

text: CXCR3- CCR8+ CCR6- CCR4+

text: Homo sapiens

characteristic: title


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: T-helper 9 cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: normal

text: wild type genotype

text: clonal culture

text: D

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: CXCR3- CCR8+ CCR6- CCR4+

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: T-helper 9 cell

text: human

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: clonal culture

characteristic: growth condition

text: E

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: CXCR3- CCR8+ CCR6- CCR4+

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Institute of Geochemistry, Chinese Academy of Sciences

characteristic: collection date

text: tobacco farmland

characteristic: environment (biome)

text: Greenhouse

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)

text: 26.9 N

characteristic: geographic location (latitude)

text: 107.1 E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: Effects of biochar on Cd and Pb mobility and microbial community composition in a calcareous soil planted with tobacco

characteristic: project name

text: soil metagenome

text: Miseq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: The BC-amended soil polluted with Cd and Pb


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institute of Geochemistry, Chinese Academy of Sciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: tobacco farmland

text: Greenhouse

text: Soil

text: China

text: 26.9 N

text: 107.1 E

text: metagenome

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Miseq

text: soil

characteristic: title


E-MTAB-6170:Sample 1

characteristic: External Id

text: Shandong Agriculture University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6170:Sample 1

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

characteristic: cultivar

text: Protocols: The siliques at 0, 1 and 2 days after pollination of wild type and atbud13-/+-1 plants grown on LD conditions were pooled together and used for Solexa Sequencing Arabidopsis plants of wild type and mutant grow under normal long day conditions (16 h light/ 8 h dark). Total RNA was isolated using mirVana™ miRNA ISOlation Kit (AM1561, Thermo Scientific, Wilmington, Delaware, USA) The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

characteristic: description

text: early embryo from 2 cell to globule embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

characteristic: organism part

text: Arabidopsis thaliana

text: 0, 1 and 2 days anthesis

characteristic: time

text: Sample 1


E-MTAB-6170:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Shandong Agriculture University

characteristic: INSDC last update

text: public

text: E-MTAB-6170:Sample 2

text: ArrayExpress

text: thale cress

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: 0, 1 and 2 days anthesis

text: Sample 2


E-MTAB-6170:Sample 3

text: Shandong Agriculture University

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6170:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: AtBUD13 heterozygous knockout

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: 0, 1 and 2 days anthesis

text: Sample 3


E-MTAB-6170:Sample 4

characteristic: External Id

text: Shandong Agriculture University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6170:Sample 4

text: ArrayExpress

text: thale cress

text: AtBUD13 heterozygous knockout

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: seed

text: Arabidopsis thaliana

text: 0, 1 and 2 days anthesis

text: Sample 4

characteristic: title


text: public

tag: Namespace:Research Center for Bio Systems, Land Use, and Nutrition (IFZ)

text: metagenome

text: metagenome

text: Pollen sample library


text: Research Center for Bio Systems, Land Use, and Nutrition (IFZ)

text: public

text: metagenome

text: metagenome

text: Pollen sample library


text: Wellcome Trust Sanger Institute

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Cells were grown to a final concentration of 5x107 cells for each ChIP-seq experiment. To stabilize Dpf2 on chromatin, cells were treated with 2 mM disuccinimidyl glutarate (DSG) for 10 minutes prior to formaldehyde crosslinking. For all other targets, cells were chemically cross-linked at room temperature by the addition of formaldehyde to 1% final concentration for 10 minutes and quenched with 0.125 M final concentration of glycine. Cross-linked cells were re-suspended in sonication buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS) and sonicated using a Diagenode Bioruptor for three 10-minute rounds using pulsing settings (30 sec ON; 1 min OFF). 10 µg of sonicated chromatin was then incubated overnight at 4ºC with 5 µg of Flag antibody conjugated to magnetic beads. Following the IP, beads were washed twice with RIPA buffer (50mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA, 1% NP-40, 0.1% Na-deocycholate, 0.1% SDS), low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10mM Tris pH 8.1, 250mM LiCl, 1mM EDTA, 1% Na-deoxycholate, 1% NP-40), and 1X TE. Finally, DNA was extracted by reverse crosslinking at 65ºC overnight with proteinase K (20ug/µL) and 1% SDS followed by phenol:chloroform:isoamyl alcohol purification and ethanol precipitation. Libraries were constructed as indicated above and sequenced using Illumina HiSeq 2500. ChIPed DNA was purified using Qiagen MinElute PCR Purification Kit. Library DNA was purified using AmpureXP beads using 1:1 ratio. Libraries were constructed using Diagenode MicroPlex ChIP kit.

characteristic: description

text: normal

characteristic: disease

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: normal

text: Dpf2 flox/flox

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

characteristic: organism part

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus


characteristic: External Id

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Protocols: Cells were grown to a final concentration of 5x107 cells for each ChIP-seq experiment. To stabilize Dpf2 on chromatin, cells were treated with 2 mM disuccinimidyl glutarate (DSG) for 10 minutes prior to formaldehyde crosslinking. For all other targets, cells were chemically cross-linked at room temperature by the addition of formaldehyde to 1% final concentration for 10 minutes and quenched with 0.125 M final concentration of glycine. Cross-linked cells were re-suspended in sonication buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS) and sonicated using a Diagenode Bioruptor for three 10-minute rounds using pulsing settings (30 sec ON; 1 min OFF). 10 µg of sonicated chromatin was then incubated overnight at 4ºC with 5 µg of Flag antibody conjugated to magnetic beads. Following the IP, beads were washed twice with RIPA buffer (50mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA, 1% NP-40, 0.1% Na-deocycholate, 0.1% SDS), low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10mM Tris pH 8.1, 250mM LiCl, 1mM EDTA, 1% Na-deoxycholate, 1% NP-40), and 1X TE. Finally, DNA was extracted by reverse crosslinking at 65ºC overnight with proteinase K (20ug/µL) and 1% SDS followed by phenol:chloroform:isoamyl alcohol purification and ethanol precipitation. Libraries were constructed as indicated above and sequenced using Illumina HiSeq 2500. The Dpf2 targeting vector was linearized and electroporated into R26::CreERT2 E14 cells to generate heterozygous ES cell lines after G418 selection. The selected heterozygous ES lines were transiently transfected with a FLP recombinase encoding plasmid (pCAGGsFlpE), converting the initial knockout allele (Dpf2+/-, lacZ positive, G418 resistant) into a “wild-type” (WT) allele with two floxP sites flanking exon 4 (Dpf2+/+, reverted WT (rWT), lacZ negative, G418 sensitive). Multiple independent rWT ES clones were then electroporated with the original Dpf2 knockout vector or Dpf2 critical exon-deleted targeting vector and selected with G418. Dpf2 critical-exon-deleted vector was generated by transforming Dpf2 targeting vector into the cre-containing bacteria. In the second round targeting, the clones recovered were only those with the second WT allele being targeted, which were confirmed by the presence of both the rWT allele and the second knockout allele. The long-range PCR reactions were carried out for genotyping (SequalPrep Long PCR kit, Invitrogen). The selected heterogeneous ES cell lines were converted to the conditional Dpf2+/+ and Dpf2+/- clones by transiently transfected with FlpE. ChIPed DNA was purified using Qiagen MinElute PCR Purification Kit. Library DNA was purified using AmpureXP beads using 1:1 ratio. Libraries were constructed using Diagenode MicroPlex ChIP kit.

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: inner cell mass

text: Mus musculus


text: Wellcome Trust Sanger Institute

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

text: house mouse

text: normal

text: Dpf2 flox/flox

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

characteristic: title


text: public

tag: Namespace:MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

characteristic: collection date

text: Metagenome sequenced from bulk DNA extraction from the deep sea mussel Bathymodiolus azoricus. The mussel was sampled on the Lucky Strike Hydrothermal vent field on the mid Atlantic Ridge.

characteristic: description

text: Hydrothermal vent

characteristic: environment (biome)

text: Black smoker

characteristic: environment (feature)

text: Sea water

characteristic: environment (material)

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Mid Atlantic Ridge - Lucky Strike

characteristic: geographic location (region and locality)

text: Bathymodiolus azoricus

characteristic: host common name

text: Adult

characteristic: host life stage

characteristic: host subject id

text: Metagenome

characteristic: investigation type

text: Bathymodiolus azoricus

text: Metagenome of 'Bathymodiolus' azoricus

characteristic: project name

text: ROV

characteristic: sample collection device or method

text: The gills were dissected and fixed in RNA later overnight at 4 C. The buffer was then drained and stored at -80 C.

characteristic: sample material processing

characteristic: sample storage temperature

text: Bathymodiolus azoricus

text: Illumina

characteristic: sequencing method

text: Gill

characteristic: tissue type

text: Metagenome from Bathymodiolus azoricus gill tissue


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PUBLIC HEALTH ENGLAND

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:PUBLIC HEALTH ENGLAND

characteristic: Submitter Id

characteristic: broker name

characteristic: description

text: Neisseria meningitidis

characteristic: organism

text: Neisseria meningitidis

characteristic: title


text: Klebsiella pneumoniae

tag: attribute

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Klebsiella pneumoniae

characteristic: common name

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: subject id


text: Enterococcus faecium

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Enterococcus faecium

text: Enterococcus faecium

text: Enterococcus faecium


text: Enterococcus faecalis

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:TECHNICAL UNIVERSITY OF DENMARK, NATIONAL VETERINARY INSTITUTE

text: pJM1-like plasmid from V. anguillarum serovar O1

text: Vibrio anguillarum serovar O1

text: Vibrio anguillarum serovar O1


characteristic: External Id

text: TECHNICAL UNIVERSITY OF DENMARK, NATIONAL VETERINARY INSTITUTE

text: public

text: Vibrio anguillarum serovar O1

text: Vibrio anguillarum serovar O1


text: Yeast

characteristic: ArrayExpress-PHENOTYPE

text: Saccharomyces cerevisiae

text: SC

characteristic: INSDC center name

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Yeast

characteristic: phenotype

text: Saccharomyces cerevisiae


text: UNIVERSITY OF EXETER

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:UNIVERSITY OF EXETER

text: Isolated from swamp grass leaf

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: Genomic sequence of Magnaporthe oryzae isolated from Bangladesh in 2016 and 2017


text: UNIVERSITY OF EXETER

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Isolated from wheat seed

text: Magnaporthe oryzae

text: Magnaporthe oryzae


text: JLU

text: public

text: Pseudomonas syringae pv. persicae CFBP 1573P

characteristic: description

text: Pseudomonas syringae pv. persicae

characteristic: organism

text: Pseudomonas syringae pv. persicae

text: P. syringae pv. persicae CFBP 1573P


NCPPB 2254

text: JLU

text: public

text: NCPPB 2254

text: Pseudomonas syringae pv. persicae NCPPB 2254

text: Pseudomonas syringae pv. persicae

text: Pseudomonas syringae pv. persicae

text: P. syringae pv. persicae NCPPB 2254

characteristic: title


text: JLU

text: public

text: Pseudomonas syringae pv. syringae CFBP 2118

text: Pseudomonas syringae pv. syringae

text: Pseudomonas syringae pv. syringae

text: P. syringae pv. syringae CFBP 2118


text: JLU

text: public

text: Pseudomonas syringae pv. syringae CFBP 4215

text: Pseudomonas syringae pv. syringae

text: Pseudomonas syringae pv. syringae

text: P. syringae pv. syringae CFBP 4215


text: JLU

text: public

text: Pseudomonas syringae pv. cerasicola CFBP 6109

text: Pseudomonas syringae pv. cerasicola

text: Pseudomonas syringae pv. cerasicola

text: P. syringae pv. cerasicola CFBP 6109


text: JLU

text: public

text: Pseudomonas syringae pv. cerasicola CFBP 6110

text: Pseudomonas syringae pv. cerasicola

text: Pseudomonas syringae pv. cerasicola

text: P. syringae pv. cerasicola CFBP 6110


text: JLU

text: public

text: Pseudomonas syringae pv. avii CFBP 3846

text: Pseudomonas syringae pv. avii

text: Pseudomonas syringae pv. avii

text: P. syringae pv. avii CFBP 3846


text: JLU

text: public

text: Pseudomonas cerasi PL963

text: Pseudomonas cerasi

text: Pseudomonas cerasi

text: P.cerasi PL963


text: NEWCASTLE UNIVERSITY

text: public

tag: Namespace:NEWCASTLE UNIVERSITY

text: AACGCACGCTAG

characteristic: barcode

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AACTCGTCGATG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AACTGTGCGTAC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AAGAGATGTCGA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AAGCTGCAGTCG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AATCAGTCTCGT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AATCGTGACTCG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACACTATGGC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACATGTCTAC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACGAGCCACA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACGGTGTCTA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACTAGATCCG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACTGTTCATG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGACCACTCA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGAGTCGGCT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGCAGTGGTC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGCTAGCTTG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGTGCTTCAT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGTTGCGCGA

text: T0 G2b

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATCACTTAGC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATGATCGTTC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATGTCACGTG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATTCAGCGCA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCAGACGATGC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCAGCGACTAG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCGCAGAGTCA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCTCGATCAGA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCTGTCTCTCT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGACGTCTTAG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGAGTGCTATC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGATGCGACCA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGCAACTGCTA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGCGATACTGG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGCGCAGATAC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGCTATCTGGA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGCTCATGGAT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGGATCGTCAG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGGTGAGTGTC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGTACTCAGTG

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGTCTGTAGCA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGTGAGAGAAT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGTGCCGTAGA

text: T56 G2b

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACGTTAGCACAC

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACTACAGCCTAT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACTACGTGTGGT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACTAGCTCCATA

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AACGCACGCTAG

text: SAND1 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AACTCGTCGATG

text: SAND1 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AACTGTGCGTAC

text: SAND1 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AAGAGATGTCGA

text: SAND1 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AAGCTGCAGTCG

text: SAND2 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AATCAGTCTCGT

text: SAND2 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: AATCGTGACTCG

text: SAND2 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACACTATGGC

text: SAND2 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACATGTCTAC

text: GAC1 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACGAGCCACA

text: GAC1 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACGGTGTCTA

text: GAC1 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACTAGATCCG

text: GAC1 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACACTGTTCATG

text: GAC2 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGACCACTCA

text: GAC2 TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGAGTCGGCT

text: GAC2 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGCAGTGGTC

text: GAC2 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGCTAGCTTG

text: SAND STR TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGTGCTTCAT

text: SAND STR TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACAGTTGCGCGA

text: SAND STR1 BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATCACTTAGC

text: SAND STR BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATGATCGTTC

text: GAC STR TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATGTCACGTG

text: GAC STR TOP

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACATTCAGCGCA

text: GAC STR BOT

text: biofilm metagenome

text: biofilm metagenome


text: NEWCASTLE UNIVERSITY

text: public

text: ACCACATACATC

text: GAC STR BOT

text: biofilm metagenome

text: biofilm metagenome


text: public

tag: Namespace:Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology

unit: day

characteristic: age

text: Maxgro (Hermitage Genetics) x (German Landrace x Large White)

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: common name

text: Protocols: The slaughter of animals, fasted for 18 hours with an average final body weight of 99 kg (SD: 11.4kg), occurred on 2 slaughter days a week apart by electronic stunning followed by exsanguination. Samples of the LTL muscle were collected and snap frozen in liquid nitrogen within 10 minutes post-mortem (pm) followed by storage at -80°C until RNA isolation. Residual feed intake is one method of measuring feed efficiency. In this study, residual feed intake (RFI) is described as the difference between actual feed intake and predicted feed requirements on product quality of the porcine Longissimus thoracis et lumborum (LTL) muscle. Pigs were placed on test between day 42 and 91 post-weaning, whereby feed intake was recorded daily, and pig weight, back-fat depth and muscle depth was recorded weekly. Average daily feed intake (ADFI) and average daily gain (ADG) from day 42 to day 91 post-weaning were calculated for each pig weekly. RFI was calculated at the end of the test period as the residual from a least squares regression model of ADFI on ADG, metabolic live weight, gender and also all relevant two-way interactions, and the effects of back-fat and muscle depth using the PROC REG procedure in SAS (version 9.4; SAS Inst. Inc., Cary, NC, USA). Total RNA was isolated using Tri-Reagent (Sigma-Alrich, Taufkirchen, Germany), followed by DNase treatment and a column-based purification using the Nucleospin RNA II kit (Macherey-Nagel, Düren, Germany). RNA library preparation was carried out using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracis muscle

characteristic: organism part

text: low residual feed intake

text: Sus scrofa

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: pig

text: normal

text: wild type genotype

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracis muscle

text: low residual feed intake

characteristic: phenotype

text: Sus scrofa

text: male


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: pig

characteristic: description

text: normal

text: wild type genotype

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracis muscle

text: high residual feed intake

text: Sus scrofa

text: male

characteristic: title


text: public

characteristic: age

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: common name

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracis muscle

text: high residual feed intake

text: Sus scrofa

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: pig

text: normal

text: wild type genotype

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracis muscle

characteristic: organism part

text: low residual feed intake

text: Sus scrofa

text: female

characteristic: sex


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: pig

text: normal

text: wild type genotype

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracis muscle

text: highresidual feed intake

characteristic: phenotype

text: Sus scrofa

text: male


text: JLU

text: public

characteristic: Submitter Id

text: Pseudomonas syringae pv. morsprunorum CFBP 6411

characteristic: description

text: Pseudomonas syringae group genomosp. 3

characteristic: organism

text: Pseudomonas syringae group genomosp. 3

text: P. syringae pv. morsprunorum CFBP 6411

characteristic: title


text: JLU

text: public

text: Pseudomonas P. syringae pv. morsprunorum CFBP 3800

text: Pseudomonas syringae group genomosp. 3

text: Pseudomonas syringae group genomosp. 3

text: P. syringae pv. morsprunorum CFBP 3800


text: JLU

text: public

text: Pseudomonas syringae pv. morsprunorum CFBP 2116

text: Pseudomonas syringae

text: Pseudomonas syringae

text: P. syringae pv. morsprunorum CFBP 2116


text: JLU

text: public

text: Pseudomonas P. syringae pv. morsprunorum CFBP 3840

text: Pseudomonas syringae

text: Pseudomonas syringae

text: P. syringae pv. morsprunorum CFBP 3840


text: EBC

text: public

characteristic: collection date

text: deep terrestrial biosphere

characteristic: environment (biome)

text: deep aquifer

characteristic: environment (feature)

text: aquatic

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenomes

text: 16SrRNA amplicon metagenomes of three deep aquifers located at the Äspö HRL

characteristic: project name

text: metagenomes

text: Illumina Miseq

characteristic: sequencing method

text: water

characteristic: water environmental package