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text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Challange poultry feces

text: chicken

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Italy

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: LSA-challenge poultry feces

characteristic: project name

text: metagenome

text: shotgun

characteristic: sequencing method


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF ZURICH

text: public

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF ZURICH

characteristic: Submitter Id

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


characteristic: External Id

text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: challenge poultry feces

text: Chicken

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

unit: DD

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: shot gun


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LSA-DISTAL-UNIBO

text: public

text: challenge poultry feces

text: chicken

text: feces

text: feces

characteristic: environment (material)

text: Italy

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: LSA-challenge poultry feces

characteristic: project name

text: metagenome

text: shotgun

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: upflow anaerobic sludge blanket reactor

text: upflow anaerobic sludge blanket reactor effluent

text: water

text: Finland

text: mimarks-survey

text: uncultured archaeon

characteristic: organism

text: anaerobic

characteristic: oxygenation status of sample

characteristic: ph

text: MIWARE

text: upflow anaerobic sludge blanket reactor

characteristic: reactor type

text: uncultured archaeon

text: Iontorrent PGM

text: Microbial community structure and functions in ethanol-fed sulphate removal bioreactors for treatment of mine water

characteristic: title

text: mine water from a clarification pond

characteristic: wastewater type

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: VTT

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: upflow anaerobic sludge blanket reactor

characteristic: environment (biome)

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: uncultured bacterium

text: anaerobic

text: MIWARE

text: upflow anaerobic sludge blanket reactor

text: uncultured bacterium

text: Iontorrent PGM

text: mine water from a clarification pond

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: upflow anaerobic sludge blanket reactor

text: water

text: Finland

text: mimarks-survey

characteristic: investigation type

text: uncultured fungus

characteristic: organism

text: anaerobic

characteristic: oxygenation status of sample

characteristic: ph

text: MIWARE

characteristic: project name

text: upflow anaerobic sludge blanket reactor

text: uncultured fungus

text: Iontorrent PGM

characteristic: sequencing method

text: mine water from a clarification pond

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: VTT

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: fluidized bed reactor

characteristic: environment (biome)

text: fluidized bed reactor effluent

text: water

text: Finland

text: mimarks-survey

text: uncultured archaeon

text: anaerobic

text: MIWARE

text: fluidized bed reactor

characteristic: reactor type

text: uncultured archaeon

text: Iontorrent PGM

characteristic: title

text: mine water from a clarification pond

characteristic: wastewater type

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: fluidized bed reactor

text: fluidized bed reactor effluent

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured bacterium

text: anaerobic

text: MIWARE

text: fluidized bed reactor

text: uncultured bacterium

text: Iontorrent PGM

text: mine water from a clarification pond

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: VTT

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: fluidized bed reactor

text: fluidized bed reactor effluent

text: water

text: Finland

text: mimarks-survey

text: uncultured fungus

characteristic: organism

text: anaerobic

characteristic: oxygenation status of sample

characteristic: ph

text: MIWARE

characteristic: project name

text: fluidized bed reactor

text: uncultured fungus

text: Iontorrent PGM

characteristic: sequencing method

text: mine water from a clarification pond

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: granular sludge

characteristic: environment (biome)

text: granular sludge

characteristic: environment (feature)

text: granular sludge

text: Finland

text: mimarks-survey

text: uncultured archaeon

text: anaerobic

text: MIWARE

text: granular sludge

characteristic: reactor type

text: uncultured archaeon

text: Iontorrent PGM

characteristic: title

text: granular sludge

characteristic: wastewater type

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: VTT

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: granular sludge

text: granular sludge

text: granular sludge

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured bacterium

text: anaerobic

text: MIWARE

text: granular sludge

text: uncultured bacterium

text: Iontorrent PGM

text: granular sludge

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: granular sludge

characteristic: environment (biome)

text: granular sludge

text: granular sludge

text: Finland

text: mimarks-survey

text: uncultured fungus

characteristic: organism

text: anaerobic

characteristic: oxygenation status of sample

characteristic: ph

text: MIWARE

characteristic: project name

text: granular sludge

text: uncultured fungus

text: Iontorrent PGM

characteristic: sequencing method

text: granular sludge

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Department of Animal Science, Iowa State University

unit: day

characteristic: age

text: Leghorn

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: chicken

characteristic: common name

text: Protocols: Chickens were euthanized with sodium pentobarbital solution. Spleen tissues were collected from four chickens randomly selected within each group in each line at 2 and 6 dpi and placed into RNAlater solution (ThermoFisher Scientific) for short-term storage and transferred to a -80°C freezer. Fayoumi and Leghorn chickens at the same age were initially raised in normal condition after hatch with ad libitum to feed and water. At 21 days posthatch (dph), each chicken line was randomly divided into two groups. One group was treated with LaSota lentogenic stain of NDV (200 ul of 107 EID50%) through nasal and ocular inoculation routes (50 ul into each eye and nostril), while the other was control group treated with 200ul Phosphate-buffered saline (PBS) through the same routes. RNA samples were isolated from spleens using Ambion MagMax-96 Kit (AM1839) (Applied Biosystems, Foster City, CA) following the manufacturer’s protocol. Proper quantity and quality of the RNA samples were ensured respectively through assessment by NanoDrop ND-1000 UV-vis spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and RNA 6000 Nano kit in Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA). Transcriptome library of each sample was constructed with 0.5 µg total RNA using Illumina TruSeq RNA sample preparation kit (Illumina Inc., San Diego, CA) following the low sample protocol in TruSeq RNA sample preparation v2 guide (Part #15026495, March 2014). The proper length of cDNA in each library was ensured by running DNA 1000 assay in Agilent 2100 Bioanalyzer.

characteristic: description

text: Gallus gallus

text: Gallus gallus

text: spleen

characteristic: organism part

text: susceptible to Newcastle disease virus infection

characteristic: phenotype

text: Gallus gallus

text: female

characteristic: sex

characteristic: title

type: has member


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Animal Science, Iowa State University

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Leghorn

text: ArrayExpress

text: chicken

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: spleen

text: Gallus gallus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Leghorn

text: ArrayExpress

text: chicken

text: Gallus gallus

text: Gallus gallus

text: spleen

text: Gallus gallus

text: female


text: public

characteristic: INSDC status

characteristic: age

text: Fayoumi

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: chicken

text: Gallus gallus

text: Gallus gallus

text: spleen

text: resistant to Newcastle disease virus infection

text: Gallus gallus

text: male


text: public

text: Fayoumi

text: ArrayExpress

text: chicken

characteristic: common name

characteristic: description

text: Gallus gallus

text: Gallus gallus

text: spleen

characteristic: organism part

characteristic: phenotype

text: Gallus gallus

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Department of Evolutionary Biology and Environmental Studies

text: Escherichia coli

text: Escherichia coli

text: E. coli W recipient exposed to W donor

characteristic: title


text: Department of Evolutionary Biology and Environmental Studies

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Escherichia coli

text: Escherichia coli

text: E. coli W recipient exposed to W donor


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LSA-DISTAL-UNIBO

text: public

characteristic: collection date

text: Challange poultry feces

text: chicken

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

text: LSA-challenge poultry feces

characteristic: project name

text: metagenome

text: shotgun

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Challange poultry feces

characteristic: description

text: Chicken

text: feces

text: feces

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LSA-DISTAL-UNIBO

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Challenge poultry feces

text: Chicken

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun


text: public

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: K recipient Ancestor


characteristic: ENA-LAST-UPDATE

text: public

text: Escherichia coli

text: Escherichia coli

text: W recipient ancestor


characteristic: External Id

text: public

text: Escherichia coli

text: Escherichia coli

text: B donor ancestor


characteristic: INSDC center name

text: public

text: Escherichia coli

text: Escherichia coli

text: W donor ancestor


characteristic: INSDC first public

text: public

text: Escherichia coli

text: Escherichia coli

text: K donor ancestor


text: LSA-DISTAL-UNIBO

characteristic: INSDC last update

text: public

text: Challange poultry feces

text: Chicken

text: Feces

text: Feces

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: LSA-challenge poultry feces

characteristic: project name

text: metagenome

text: shotgun

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Escherichia coli

text: Escherichia coli

text: E. coli W recipient exposed to no donors

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LSA-DISTAL-UNIBO

text: public

characteristic: collection date

text: Challenge poultry feces

characteristic: description

text: Chicken

characteristic: environment (biome)

text: Feces

characteristic: environment (feature)

text: Feces

characteristic: environment (material)

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

characteristic: organism

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun


text: UZ KU Leuven

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:UZ KU Leuven

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Center for Environmental Sciences

text: public

tag: Namespace:Center for Environmental Sciences

text: terrestrial biome

text: environmental zone

text: soil

text: Bulgaria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Pistacia terebinthus

text: plant-associated

characteristic: plant-associated environmental package

text: Drought

characteristic: project name

text: Pistacia terebinthus

text: Illumina shotgun

characteristic: sequencing method

text: Soil samples for bacterial communities


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: THE ROSLIN INSTITUTE

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:THE ROSLIN INSTITUTE

characteristic: Submitter Id

text: metagenome

text: 2013E Luing Medium Concentration Diet Low Emitter High Feed Conversion Ratio

characteristic: description

text: metagenome

text: metagenome

characteristic: title


text: THE ROSLIN INSTITUTE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: metagenome

characteristic: common name

text: 2013E Luing Medium Concentration Diet Low Emitter Low Feed Conversion Ratio

text: metagenome

characteristic: organism

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Charolais Medium Concentration Diet High Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Charolais Medium Concentration Diet High Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Luing High Concentration Diet Low Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Charolais High Concentration Diet Low Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Charolais High Concentration Diet Low Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Luing High Concentration Diet Low Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Luing Medium Concentration Diet High Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Luing Medium Concentration Diet High Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Luing Medium Concentration Diet Low Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Limousin Medium Concentration Diet High Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Aberdeen Angus Medium Concentration Diet High Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Aberdeen Angus Medium Concentration Diet Low Emitter Low Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Aberdeen Angus Medium Concentration Diet High Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Limousin Medium Concentration Diet High Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2014E Limousin Medium Concentration Diet Low Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: THE ROSLIN INSTITUTE

text: public

text: metagenome

text: 2013E Limousin Medium Concentration Diet High Emitter High Feed Conversion Ratio

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: prokaryotic 16S rRNA marker sequencing on Norway spruce needle samples replicate 2

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: prokaryotic 16S rRNA marker sequencing on Norway spruce needle samples

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: prokaryotic 16S rRNA marker sequencing on Norway spruce fine root samples

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: prokaryotic 16S rRNA marker sequencing of boreal mor layer samples

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: fungal ITS region sequencing on Norway spruce needle samples

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: fungal ITS region sequencing on Norway spruce fine root samples

text: metagenome

text: metagenome


text: UPSC

text: public

text: metagenome

text: fungal ITS region sequencing of boreal mor layer samples

text: metagenome

text: metagenome


text: human metagenome

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human metagenome

text: human metagenome

text: human metagenome

characteristic: subject id


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


name: 1 - 5mC MedIP-Seq from maternally deprived rats

text: Luxembourg Institute of Health

text: public

tag: Namespace:Luxembourg Institute of Health

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Genome-wide 5mC DNA profile of the hippocampus of maternally deprived rats


2 - 5mC MedIP-Seq from handled rats

text: Luxembourg Institute of Health

text: public

text: 2 - 5mC MedIP-Seq from handled rats

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Genome-wide 5mC DNA profile of the hippocampus of handled rats


name: 4 - 5hmC MedIP-Seq from maternally deprived rats

text: Luxembourg Institute of Health

text: public

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Genome-wide 5hmC DNA profile of the hippocampus of maternally deprived rats


5 - 5hmC MedIP-Seq from handled rats

text: Luxembourg Institute of Health

text: public

text: 5 - 5hmC MedIP-Seq from handled rats

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Genome-wide 5hmC DNA profile of the hippocampus of handled rats


text: THE CATHOLIC UNIVERSITY OF KOREA

text: public

tag: Namespace:THE CATHOLIC UNIVERSITY OF KOREA

characteristic: collection date

text: stool

characteristic: environment (biome)

text: stool

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: prokaryote enrichment culture

characteristic: project name

text: prokaryote enrichment culture

text: Miseq

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: JUSTUS LIEBIG UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:JUSTUS LIEBIG UNIVERSITY

characteristic: Submitter Id

text: E. Coli

characteristic: common name

text: ST131 blaCTX-M-27

characteristic: description

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Centrum Medyczne Ksztalcenia Podyplomowego

text: house mouse

text: sepsis

text: kidney

characteristic: organ

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: time


text: Centrum Medyczne Ksztalcenia Podyplomowego

text: public

text: house mouse

text: sepsis

text: kidney

text: Mus musculus

text: Mus musculus


text: public

text: house mouse

text: control

text: kidney

text: Mus musculus

text: Mus musculus


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


text: Streptococcus pneumoniae

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: GPS_NG_BH 2795


text: EMBL Heidelberg

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-57321499418358:Rad21_ES_FBS_rep1_Rad21

tag: Namespace:EMBL Heidelberg

text: abcam ab992

characteristic: antibody

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Sox1-GFP mouse embryonic stem cells derived from the E14tg2a line (46C) were grown at 37 °C in a 5% (v/v) CO2 incubator in GMEM (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 ng/ml leukemia inhibitory factor (LIF, in-house), 1 mM 2-mercaptoethanol, non-essential amino acids (Gibco), L-glutamine (Gibco) and Na-pyruvate (Gibco), on gelatin-coated (0.1% v/v) dishes. Accutase (Sigma) was used for cell dissociation and diluted with cell culture medium according to the manufacturer’s recommendations. Cells were passaged every second day and seeded at a density of 1.3 million cells per 10 cm in diameter culture vessel. Medium was exchanged daily. Cells were crosslinked with 1% formaldehyde for 10min at RT, glycine was added to a final concentration of 0.125M to quench formaldehyde. Cells were lysed with 1 ml of lysis buffer (10 mM Tris pH 7.5, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitors) for 20 minutes on ice. Chromatin was sonicated to average fragment size of 400bp. Chromatin extracts corresponding to 10M of cells (90µg of DNA) were precleared with 40µl of Protein A dynabeads. The sample was incubated at 4°C with overhead mixing for 1 hour. 40µl of protein A Dynabeads was washed with PBS and incubated with anti-CTCF (Milipore, 07-729, 5µl) or anti-Rad21 (Abcam, ab-992, 5µg) at RT with overhead mixing (40µl of beads per 5µl of anti-CTCF or 5µg of anti Rad21). 500µl of pre-cleared chromatin was mixed with the antibody-coupled beads and incubated overnight at 4°C with overhead mixing. Next, beads were washed for 10 minutes at 4°C with overhead mixing with lysis buffer (2x), lysis buffer containing 0.3M NaCl (2x), LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate, 2x), TE (pH 8.0) plus 0.2% Triton X-100, and TE (pH 8.0). Beads were resuspended in 100µl of TE (pH 8) and incubated at 65°C for 14 hours, 1µl of RNAseA was added and the sample incubated for 1 hour at 37°C. Next,10µl of Proteinase K was added and the sample incubated at 55°C for 2 hours. Beads were separated from the solution using a magnet. 110µl of the supernatant was mixed with 200µl of Ampure Beads (Beckman Coulter) and DNA was extracted following manufacturer’s suggestions. The Library was prepared in Ovation SP Ultralow library system (Nugen) using 2ng of ChIP material.

text: FBS

characteristic: growth condition

text: Mus musculus

text: Mus musculus

text: naive embryonic stem cell

characteristic: progenitor cell type

characteristic: replicate

text: Mus musculus


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text: E-MTAB-57321499418358:Rad21_ES_FBS_rep2_Rad21

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text: abcam ab992

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

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text: FBS

text: Mus musculus

text: Mus musculus

text: naive embryonic stem cell

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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: RUHR-UNIVERSITY BOCHUM

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: uncultured fungus

characteristic: common name

text: Leaf

characteristic: description

text: beech forest

text: forest

text: Leaf

text: Germany

text: host-associated

text: metagenome

text: uncultured fungus

text: EnDeco

text: uncultured fungus

text: Illumina

text: ITS

characteristic: title


characteristic: External Id

text: UZ KU Leuven

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: 78X28 affected individual (L084 XLID family)


text: UNIVERSITY OF LAUSANNE

text: public

tag: Namespace:UNIVERSITY OF LAUSANNE

characteristic: collection date

text: Sandy Soil from St. Sulpice with added Succinate as extra carbon source

text: Soil

characteristic: environment (biome)

text: Sand

characteristic: environment (feature)

text: Sand

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

characteristic: investigation type

text: Pseudomonas veronii

text: Metatranscriptomic response of soil microbial communties

characteristic: project name

text: Pseudomonas veronii

text: Illumina

text: soil

characteristic: soil environmental package

text: Metatranscriptomic of soil microbial communities


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UZ KU Leuven

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: L061_S unaffected individual (L061 XLID family)

characteristic: title


characteristic: External Id

text: UZ KU Leuven

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: L061_Y affected individual (L061 XLID family)


text: Glasgow Polyomics

text: public

tag: Namespace:Glasgow Polyomics

text: house mouse

text: Mus musculus

text: Mus musculus

text: Identification of Sertoli cell-specific transcripts in the mouse testis and the role of FSH and androgen in the control of Sertoli cell activity


MEAE

text: CEES

text: public

text: MEAE

text: haddock

text: Melanogrammus aeglefinus

text: Melanogrammus aeglefinus

text: Genome sequencing of haddock


text: UZ KU Leuven

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: 5X15 unaffected individual (L020 XLID family)


text: LSA-DISTAL-UNIBO

text: public

characteristic: collection date

text: Challenge poultry feces

characteristic: description

text: Chicken

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UZ KU Leuven

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens

text: 5X20 affected individual (L020 XLID family) SMRTcells2-6


characteristic: External Id

text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Challenge poultry feces

text: Chicken

text: Feces

text: Feces

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: organism

text: LSA-challenge poultry feces

characteristic: project name

text: metagenome

text: Shotgun

characteristic: title


text: URMITE

text: public

text: Klebsiella sp. 2680

text: Klebsiella sp. 2680

characteristic: strain

text: Real-time genomics to decipher atypical bacteria in clinical microbiology


text: LSA-DISTAL-UNIBO

text: public

text: Challenge Poultry feces

characteristic: description

text: Chicken

characteristic: environment (biome)

text: Feces

characteristic: environment (feature)

text: Feces

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

text: 44°26'4272 N

characteristic: geographic location (latitude)

text: 11°28'3540 E

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LSA-DISTAL-UNIBO

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Challenge poultry fecesw

text: Chicken

text: Feces

text: Feces

text: Italy

text: 44°26'4272 N

text: 11°28'3540 E

text: host-associated

text: metagenome

text: metagenome

text: LSA-challenge poultry feces

text: metagenome

text: Shotgun


text: UZ KU Leuven

characteristic: INSDC first public

text: public

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: 78X19 unaffected individual (L084 XLID family)

characteristic: title


text: public

tag: Namespace:LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE

text: Sample from continuous culture

characteristic: description

text: Leptospirillum ferriphilum

text: Leptospirillum ferriphilum


tag: attribute

text: UT SOUTHWESTERN MEDICAL CENTER

text: public

tag: Namespace:UT SOUTHWESTERN MEDICAL CENTER

text: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

text: 16S for Salmonella infected Swiss Webster Mice


E-MTAB-5860:Sample 1

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 1

tag: Namespace:DAMTP Cambridge University

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

text: Protocols: Informed consent was obtained from patients or their guardians prior to collection of venous blood from patients presenting at hospitals in Timika, Papua, Indonesia who were diagnosed with either uncomplicated or severe malaria. The blood was passed twice over CF11 cellulose columns and the purified red blood cells including malaria parasite infected red blood cells were collected in PBS, centrifuged and dissolved in ten cell pellet volumes of trizol, incubated at 37 degrees for 5 minutes and then stored at -80 degrees C. CF11 cellulose purified, infected, red blood cells dissolved in trizol and stored frozen were thawed at 37 degrees C, 0.2 x volumes of chloroform was added and samples mixed. incubated 3 min at room temperature, then centrifuged 9,000g for 30 min at 4 degrees. The supernatant was mixed with an equal volume of 70% ethanol and then applied to an RNeasy mini column (QIAGEN). Once all sample had been loaded onto the column using a vacuum manifold 0.7 ml of QIAGEN buffer RW1 was passed through the column, then 2 x 0.5 ml washes with QIAGEN buffer RPE then the column was spun for 1 min and then RNA was eluted from the dried column into a fresh tube using 2 x 0.05 ml aliquots of RNAse free water. RNA was DNased with QIAGEN DNase I in solution as per manufacturer's instructions, removal of gDNA was confirmed by Q-PCR prior to performing the RNA cleanup/DNase I removal protocol with a QIAGEN RNeasy column as per the manufacturer's instructions, RNA was eluted in 2 x 0.05 ml aliquots of RNase free water. Whole RNA integrity was confirmed using a BioRad experion and high sensitivity RNA chips. High quality samples were then depleted of hemoglobin RNA using the Ambion human Globin clear kit as per the manufacturer's instructions except that after capture of globin RNA with streptavidin magnetic beads the remnant supernatant was ethanol precipitated with 3M Na acetate pH5.5 and 0.15 mg/ml linear acrylamide at -20 degrees overnight then washed with cold 70% ethanol and dissolved in 0.05 ml RNase free water. mRNA was enriched using NEBnext Poly(A) mRNA magnetic isolation module but with elution into NEBnext Ultra Directional RNA Library Prep Kit first strand buffer for 10 min at 94 degrees. Library preparation was as per the manufacturer's instructions except that size selection was performed using Ampure XP beads at bead buffer concentrations of 0.5x and 0.8x. Library amplification was performed using 1U Kapa HiFi in 5x HiFi buffer containing TMAC, 0.3 mM each dNTP, 0.5 micromolar each primer, 3 microlitres USER enzyme, incubated at 37 degrees for 15 min, 1 min at 98 degrees then 15 cycles of (10 sec at 98 degrees and 1 min at 65 degrees), then 5 min at 65 degrees. Libraries were purified using 0.8x Ampure XP beads.

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 1


E-MTAB-5860:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 2

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 2


E-MTAB-5860:Sample 3

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 3

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 3


E-MTAB-5860:Sample 4

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 4


E-MTAB-5860:Sample 5

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 5

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 5

characteristic: title


E-MTAB-5860:Sample 6

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 6

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 6


E-MTAB-5860:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 7

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 7


E-MTAB-5860:Sample 8

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 8

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 8


E-MTAB-5860:Sample 9

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 9


E-MTAB-5860:Sample 10

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 10

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 10

characteristic: title


E-MTAB-5860:Sample 11

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 11

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 11


E-MTAB-5860:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 12

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 12


E-MTAB-5860:Sample 13

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 13

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 13


E-MTAB-5860:Sample 14

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 14

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 14


E-MTAB-5860:Sample 15

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 15

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 15

characteristic: title


E-MTAB-5860:Sample 16

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 16

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 16


E-MTAB-5860:Sample 17

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 17

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 17


E-MTAB-5860:Sample 18

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 18

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 18


E-MTAB-5860:Sample 19

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 19

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 19


E-MTAB-5860:Sample 20

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 20

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 20

characteristic: title


E-MTAB-5860:Sample 21

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 21

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 21


E-MTAB-5860:Sample 22

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 22

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 22


E-MTAB-5860:Sample 23

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 23

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: severe malarial disease

text: venous blood

text: Plasmodium falciparum

text: Sample 23


E-MTAB-5860:Sample 24

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 24

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 24


E-MTAB-5860:Sample 25

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 25

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 25

characteristic: title


E-MTAB-5860:Sample 26

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 26

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 26


E-MTAB-5860:Sample 27

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 27

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 27


E-MTAB-5860:Sample 28

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 28

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 28


E-MTAB-5860:Sample 29

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 29

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 29


E-MTAB-5860:Sample 30

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 30

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 30

characteristic: title


E-MTAB-5860:Sample 31

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 31

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 31


E-MTAB-5860:Sample 32

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 32

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 32


E-MTAB-5860:Sample 33

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 33

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 33


E-MTAB-5860:Sample 34

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 34

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 34


E-MTAB-5860:Sample 35

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 35

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 35

characteristic: title


E-MTAB-5860:Sample 36

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 36

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 36


E-MTAB-5860:Sample 37

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 37

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 37


E-MTAB-5860:Sample 38

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 38

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 38


E-MTAB-5860:Sample 39

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 39

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 39


E-MTAB-5860:Sample 40

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 40

text: ArrayExpress

characteristic: broker name

text: malaria parasite P. falciparum

characteristic: date

characteristic: description

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 40

characteristic: title


E-MTAB-5860:Sample 41

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 41

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

characteristic: disease

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

characteristic: phenotype

text: venous blood

characteristic: sampling site

text: Plasmodium falciparum

characteristic: strain

text: Sample 41


E-MTAB-5860:Sample 42

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DAMTP Cambridge University

text: public

text: E-MTAB-5860:Sample 42

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 42


E-MTAB-5860:Sample 43

text: DAMTP Cambridge University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5860:Sample 43

text: ArrayExpress

text: malaria parasite P. falciparum

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 43


E-MTAB-5860:Sample 44

text: DAMTP Cambridge University

characteristic: INSDC first public

text: public

text: E-MTAB-5860:Sample 44

characteristic: Submitter Id

text: ArrayExpress

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum malaria

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum

text: uncomplicated malaria

text: venous blood

text: Plasmodium falciparum

text: Sample 44


text: UZH

text: public

text: E-MTAB-5839:ChIP-seq_UBF_MEFs_UBFfl_Rep1

text: ArrayExpress

characteristic: broker name

text: mouse embryonic fibroblast

characteristic: cell type

text: house mouse

text: Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Nuclei were isolated using Lysis Buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), transferred to Sonication Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EGTA, 4 mM EDTA, 0.1% SDS, 1% Triton X-100, 1% NP-40) and sonicated (Bioruptor, Diagenode) for 2 cycles of 30 sec on / 30 sec off, for 15 min at high intensity. Each immunoprecipitation (IP) was carried out on the equivalent of 50 x 106 cells in IP Buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100) overnight at 4°C. The antibody slurry was prepared with 50 µl A-, 50 µl G-Dynabeads and 60 µg.ml-1 antibody per IP. Immunoprecipitated chromatin was treated with RNaseA and the DNA isolated using 2% Na SDS and 2mg.ml-1 Proteinase-K. Two or more biological replicates were analyzed for each antibody. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end sequencing on an Illumina HiSeq 2000 (McGill University and Génome Québec Innovation Centre).

characteristic: description

text: UBFfl/fl ERCre+/+ p53-/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-CHECKLIST

text: UZH

text: public

text: E-MTAB-5839:ChIP-seq_UBF_MEFs_UBFfl_4HT_Rep1

text: ArrayExpress

text: mouse embryonic fibroblast

text: house mouse

text: UBFfl/fl ERCre+/+ p53-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus