text: NTNU University Museum

text: NTNU University Museum

text: public

tag: Namespace:NTNU University Museum

characteristic: collection date

text: common ragweed

text: Seeds were collected from a natural Ambrosia artemisiifolia population in North Dakota, USA in 2008. From these seeds, the individual plant AA19_3_7 was grown to maturity in a greenhouse at the Department of Botany, University of British Columbia. Fresh leaf tissue was sampled, flash-frozen in liquid nitrogen and then stored at -80°C. High-molecular-weight (HMW) genomic DNA was extracted using a CTAB protocol and prepared for various types of sequencing.

text: USA

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: isolation and growth condition

text: Ambrosia artemisiifolia

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

characteristic: plant structure

text: Ambrosia artemisiifolia individual AA19_3_7


CTU positive control

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

characteristic: INSDC first public

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characteristic: INSDC status

characteristic: SRA accession

text: CTU positive control

tag: Namespace:QUEEN'S UNIVERSITY BELFAST

characteristic: Submitter Id

text: Illumina adapters

characteristic: adapters

text: CTU positive control

characteristic: common name

text: CTU positive control

characteristic: description

text: lab

characteristic: environment (biome)

text: lab

characteristic: environment (feature)

text: liquid

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

unit: centuries

characteristic: host age

text: host-associated

characteristic: host-associated environmental package

characteristic: investigation type

text: PCR

characteristic: nucleic acid amplification

text: metagenome

characteristic: organism

text: 95�C for 3 minutes, 20 cycles at 95�C for 30 seconds, 55�C for 30 seconds, 72�C for 30 seconds and then 72�C for 5 minutes.

characteristic: pcr conditions

text: 515F and 806R

characteristic: pcr primers

characteristic: project name

unit: °C

characteristic: sample storage temperature

unit: g

characteristic: sample volume or weight for DNA extraction

text: Illumina MiSeq

characteristic: sequencing method

text: 16S: V4- 250 bp

characteristic: target gene

text: Control

characteristic: title


Negative control

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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: Negative control

characteristic: Submitter Id

text: Illumina adapters

characteristic: adapters

characteristic: collection date

text: Negative control

characteristic: common name

text: Negative PBS control

characteristic: description

text: lab

characteristic: environment (biome)

text: liquid

characteristic: environment (feature)

text: PBS

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

text: host-associated

text: PCR

text: Fast DNA SPIN Kit for Soil

characteristic: nucleic acid extraction

text: metagenome

text: 515F and 806R

text: Illumina MiSeq

text: 16S: V4- 250 bp

text: Control


Positive control

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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QUEEN'S UNIVERSITY BELFAST

text: QUEEN'S UNIVERSITY BELFAST

text: public

text: Positive control

text: Illumina adapters

text: Positive control

text: Positive Zymo control

text: lab

text: liquid

text: Commercial mock community

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

characteristic: host age

text: host-associated

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text: Fast DNA SPIN Kit for Soil

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characteristic: organism

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characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

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characteristic: title


Rumen fluid_1_C

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text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

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characteristic: Submitter Id

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text: Rumen fluid first collection C

characteristic: description

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characteristic: environment (biome)

text: GIT

characteristic: environment (feature)

text: Rumen fluid

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

text: 8 months

text: White

characteristic: host color

text: Sheep

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text: C

characteristic: host diet

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characteristic: host sex

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text: 16S: V4- 250 bp

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Rumen fluid_1_H

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text: QUEEN'S UNIVERSITY BELFAST

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text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

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characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

text: 8 months

characteristic: host age

text: White

text: Sheep

text: H

text: male

text: host-associated

characteristic: host-associated environmental package

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characteristic: title


Rumen fluid_2_C

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text: QUEEN'S UNIVERSITY BELFAST

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characteristic: INSDC center name

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characteristic: Submitter Id

text: Illumina adapters

characteristic: adapters

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text: Rumen fluid_2_C

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text: Rumen fluid second collection C

characteristic: description

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characteristic: environment (biome)

text: GIT

characteristic: environment (feature)

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text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

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characteristic: host color

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characteristic: host common name

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characteristic: host diet

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Rumen fluid_2_H

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characteristic: External Id

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

characteristic: INSDC first public

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characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

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characteristic: host age

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text: male

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characteristic: host-associated environmental package

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characteristic: title


Rumen fluid_3_C

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text: QUEEN'S UNIVERSITY BELFAST

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characteristic: Submitter Id

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characteristic: environment (biome)

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characteristic: environment (feature)

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characteristic: geographic location (latitude)

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Rumen fluid_3_H

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characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

text: 8 months

characteristic: host age

text: White

text: Sheep

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text: male

text: host-associated

characteristic: host-associated environmental package

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characteristic: nucleic acid amplification

text: Fast DNA SPIN Kit for Soil

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characteristic: pcr primers

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characteristic: sequencing method

text: 16S: V4- 250 bp

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text: Rumen fluid

characteristic: title


Small intestine_C

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characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

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characteristic: Submitter Id

text: Illumina adapters

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text: Small intestine_C

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text: Small instestine fluid C

characteristic: description

text: Small intestine

characteristic: environment (biome)

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characteristic: environment (feature)

text: Intestinal fluid

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

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text: White

characteristic: host color

text: Sheep

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characteristic: host diet

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text: metagenome

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text: Illumina MiSeq

text: 16S: V4- 250 bp

text: Small intestine


Small intestine_H

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characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

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text: Illumina adapters

text: Small intestine_H

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text: Small intestine

text: GIT

text: Intestinal fluid

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

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characteristic: host age

text: White

text: Sheep

text: H

text: male

text: host-associated

characteristic: host-associated environmental package

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text: Fast DNA SPIN Kit for Soil

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Large intestine_C

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characteristic: INSDC center alias

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characteristic: INSDC center name

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characteristic: environment (biome)

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characteristic: geographic location (latitude)

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Large intestine_H

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characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

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characteristic: host age

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characteristic: ENA-CHECKLIST

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text: Illumina adapters

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characteristic: geographic location (latitude)

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characteristic: host color

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characteristic: ENA-CHECKLIST

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characteristic: environment (material)

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characteristic: geographic location (country and/or sea)

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characteristic: ENA-CHECKLIST

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characteristic: environment (biome)

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text: United Kingdom

characteristic: geographic location (latitude)

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characteristic: host color

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characteristic: ENA-CHECKLIST

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characteristic: environment (material)

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characteristic: target gene

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text: Illumina adapters

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characteristic: description

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characteristic: environment (biome)

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text: United Kingdom

characteristic: geographic location (latitude)

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text: White

characteristic: host color

text: Sheep

characteristic: host common name

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characteristic: host diet

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text: Fast DNA SPIN Kit for Soil

characteristic: nucleic acid extraction

text: metagenome

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

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text: Illumina adapters

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characteristic: environment (biome)

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text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

text: 6 months

text: White

characteristic: host color

text: Sheep

characteristic: host common name

text: C

characteristic: host diet

text: neuter

characteristic: host sex

text: host-associated

text: PCR

text: Fast DNA SPIN Kit for Soil

characteristic: nucleic acid extraction

text: metagenome

text: 515F and 806R

text: Illumina MiSeq

text: 16S: V4- 250 bp

text: InVitro


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Illumina adapters

text: Animal 3 O

text: Rumen

text: GIT

text: Rumen fluid

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Belfast

characteristic: geographic location (region and locality)

text: 6 months

characteristic: host age

text: White

text: Sheep

text: O

text: neuter

text: host-associated

characteristic: host-associated environmental package

characteristic: investigation type

text: PCR

characteristic: nucleic acid amplification

text: Fast DNA SPIN Kit for Soil

text: metagenome

characteristic: organism

characteristic: pcr conditions

text: 515F and 806R

characteristic: pcr primers

characteristic: project name

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: Illumina MiSeq

characteristic: sequencing method

text: 16S: V4- 250 bp

characteristic: target gene

text: InVitro

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center alias

text: QUEEN'S UNIVERSITY BELFAST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Illumina adapters

characteristic: adapters

characteristic: collection date

characteristic: common name

text: Animal 3 A

characteristic: description

text: Rumen

characteristic: environment (biome)

text: GIT

characteristic: environment (feature)

text: Rumen fluid

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Belfast

text: 6 months

text: White

characteristic: host color

text: Sheep

characteristic: host common name

text: A

characteristic: host diet

text: neuter

characteristic: host sex

text: host-associated

text: PCR

text: Fast DNA SPIN Kit for Soil

characteristic: nucleic acid extraction

text: metagenome

text: 515F and 806R

text: Illumina MiSeq

text: 16S: V4- 250 bp

text: InVitro


text: unknown

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Human

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unknown

characteristic: GENDER

text: SC

characteristic: INSDC center alias

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: unknown

characteristic: PHENOTYPE

text: human

text: Homo sapiens

characteristic: organism

characteristic: title


text: INSTITUT PASTEUR

text: Institut Pasteur

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSTITUT PASTEUR

characteristic: Submitter Id

text: Institit Pasteur du Cambodge

characteristic: collecting institution

characteristic: collection date

text: Anthony Ruberto, Caitlin Bourke

characteristic: collector name

text: malaria parasite P. vivax

characteristic: common name

text: Pools of sporozoites were dissected from salivary glands of An.dirus mosquitoes and cDNA libraries were generated using 10x Genomics single-cell gene expression technology

characteristic: description

text: Day 16

text: microscopy

characteristic: diagnostic method

text: Pv field isolate

characteristic: genotype

text: Cambodia

characteristic: geographic location (country and/or sea)

text: 11.5564 N

characteristic: geographic location (latitude)

text: 104.9282 E

characteristic: geographic location (longitude)

text: 21-25 days old

characteristic: host age

text: Anopheles dirus

characteristic: host common name

text: dead

characteristic: host disease outcome

text: not applicable

characteristic: host health state

text: Anopheles dirus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: salivary glands

characteristic: isolation source host-associated

characteristic: isolation source non-host-associated

text: human

characteristic: known pathogenicity

text: Plasmodium vivax

text: Field isolate

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center alias

text: Institut Pasteur

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Institit Pasteur du Cambodge

characteristic: collecting institution

characteristic: collection date

text: Anthony Ruberto, Caitlin Bourke

characteristic: collector name

text: malaria parasite P. vivax

characteristic: common name

characteristic: description

text: Day 18

text: microscopy

characteristic: diagnostic method

text: Pv field isolate

text: Cambodia

text: 11.5564 N

text: 104.9282 E

text: 21-25 days old

text: Anopheles dirus

text: dead

text: not applicable

text: Anopheles dirus

text: female

text: salivary glands

text: human

text: Plasmodium vivax

characteristic: organism

text: Field isolate

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR

text: Institut Pasteur

text: public

text: Institit Pasteur du Cambodge

text: Anthony Ruberto, Caitlin Bourke

text: malaria parasite P. vivax

text: Day 17

text: microscopy

text: Pv field isolate

characteristic: genotype

text: Cambodia

characteristic: geographic location (country and/or sea)

text: 11.5564 N

characteristic: geographic location (latitude)

text: 104.9282 E

characteristic: geographic location (longitude)

text: 21-25 days old

characteristic: host age

text: Anopheles dirus

characteristic: host common name

text: dead

characteristic: host disease outcome

text: not applicable

characteristic: host health state

text: Anopheles dirus

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: salivary glands

characteristic: isolation source host-associated

characteristic: isolation source non-host-associated

text: human

characteristic: known pathogenicity

text: Plasmodium vivax

text: Field isolate

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center alias

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: M. pneumoniae cells were grown in two T75 cm2 flasks and recovered in a 2ml electroporation buffer and 80 µl of cells were electroporated with 2 pmol of the different mini-transposon vectors (2 technical replicates per sample and two biological replicates). After electroporation cells were resuspended in a final volume of 1 ml by adding 900 µl of HF. The 2 transformations of each vector were pooled (total volume of 2ml). Five hundred µl of cells were cultured in 20ml of medium in a T75 flask with different concentrations of chloramphenicol (0.5, 1, 2 and 15 µg/ml) for 4 days at 37ºC in 5% CO2. After one day of incubation each flask was resuspended in 1.5 ml of medium and cells were seeded in 150 ml of medium in a T300 flask. After 48 days of growth at 37ºC in 5% CO2 DNA of samples treated with 0.5, 1, 2 µg/ml of chloramphenicol was extracted. The samples of 15 µg/ml were processed after 72 additional hours. This experiment was repeated twice and DNA samples were sequenced independently. M. pneumoniae M129 strain was grown in 75 cm2 tissue culture flasks with 50 mL of modified Hayflick medium (HF) at 37ºC and was transformed as previously described 45. To select M. pneumoniae transformant cells, plates were supplemented with 20 µg/ml chloramphenicol or 0.02 µg/ml of erythromycin. Transformed cells were also grown in liquid cultures and testing different concentrations of antibiotics. First, M. pneumoniae M129 was grown in a 96 well plate format with 200 µl of HF and 5 µl of transformed cells. For chloramphenicol the tested concentrations were 0, 0.5, 1, 2, 5, 10, 15 and 20 µg/ml. In the case of erythromycin, the tested concentrations were 0,002 and 0.02 µg/ml. Concentrations of 0.5, 1, 2, 5, 10, 15 µg/ml for chloramphenicol libraries and 0.02 µg/ml for erythromycin libraries were selected for sequencing. To study the proteome of M. pneumoniae, transformed cells were grown in T75 flasks with different antibiotic concentrations (0.5, 1, 2 and 15 µg/ml of chloramphenicol) to cover from low to highly expressed proteins. After 24 h cells were passed to a T300 cm2 flask, cultures of cells grown with 0.5, 1, 2 and 15 µg/ml of antibiotic were confluent after 48h and cultures of cells grown in 15 µg/ml required three additional days. Genomic DNAs of M. pneumoniae M129 were isolated with the Illustrabacteria genomic Kit (GE). The purification of PCR products and digested fragments from agarose gels were achieved using the QIAquick Gel Extraction Kit (Quiagen). Plasmid DNA was obtained by using the QIAprep Spin Miniprep Kit (Quiagen). Between 10 and 500 ng genomic DNA were fragmented to 200-300 bp using a Covaris S2 instrument. End repair and adaptor ligation was performed using the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer's instructions with the exception that the adaptor used contained only the read 1 adaptor sequence and not the standard Illumina Y-shaped adaptor containing read 1 and read 2 adaptor sequences. The adaptor ligated dnA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix in a 50 µL reaction with primers R1 PA primer and Tn select PA primer (0.2 µM final concentration) using the following PCR program: 98 °C, 30 seconds; 8 cycles of 98 °C, 10 seconds and 65 °C 25 seconds; followed by a final extension of 5 minutes at 65 °C. An estimation of PCR cycles required for library amplification was performed by qPCR NEBNext Q5 Hot Start HiFi PCR Master Mix in a 50 µL reaction adding SYBR Green I (10.000x in DMSO Sigma Aldrich) to the PCR reaction at 0.1x final concentration. PCR was performed in a Roche Light Cycler LC480 for 30 cycles using the same conditions as for the first PCR reaction. 1 µL of the first PCR was used as template and Universal PCR Primer (NEB) and R2 TN select nested primer mix were used at 0.2 µM final concentration. The remaining 49 µL of the first PCR were purified using 1.8x volumes of AMPure XP beads (Beckman Coulter) according to the manufacturer's protocol. The purified product was eluted in 48 µL of buffer EB (Qiagen). 15 µL of the purified first PCR product were then used for a second PCR with the number of cycles estimated from the previous qPCR (cycle number close to plateau minus 3 cycles due to the increased amount of template). PCR conditions were the same as in the qPCR using NEBNext Q5 Hot Start HiFi PCR Master Mix in a 50 µL reaction and Universal PCR Primer (NEB) and R2 TN select nested primer mix were used at 0.2 µM final concentration but omitting the SYBR Green I. The second PCR was purified using 1x volume of AMPure XP beads and eluted in 20 µL of buffer EB. To complete adaptor sequences and add sample barcodes, a third PCR was performed with NEBNext Q5 Hot Start HiFi PCR Master Mix in a 50 µL reaction using 19 µL of the purified second PCR as templates. Primers used were Universal PCR Primer and a suitable NEBNext Multiplex primer for Illumina at 0.6 uM final concentration. The PCR program used was: 98 °C, 30 seconds; 4 cycles of 98 °C, 10 seconds and 65 °C 75 seconds; followed by a final extension of 5 minutes at 65 °C. After the third PCR libraries were purified using 1x volume AMPure XP beads and eluted in 20 µL buffer EB.

characteristic: description

text: Random mutagenesis with TnP438catIR*

text: Mycoplasma pneumoniae M129

characteristic: organism

text: Mycoplasma pneumoniae M129

text: whole organism

characteristic: organism part

characteristic: title


text: CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

text: public

text: ArrayExpress

text: Random mutagenesis with Tncat*IR*

characteristic: genotype

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: Random mutagenesis with TnP438catIR**

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Random mutagenesis with Tncat*IR**

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: Random mutagenesis with TnP438catIR*

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: External Id

text: public

text: ArrayExpress

text: Random mutagenesis with Tnbar*IR*

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: INSDC center alias

text: public

text: ArrayExpress

text: Random mutagenesis with TnPSynEryIR*

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


characteristic: INSDC center name

text: public

text: ArrayExpress

text: Random mutagenesis with TnEry*IR*

text: Mycoplasma pneumoniae M129

text: Mycoplasma pneumoniae M129

text: whole organism


text: UNIVERSITY OF OXFORD

text: University of Oxford, Oxford, England, UK

characteristic: INSDC first public

text: public

tag: Namespace:UNIVERSITY OF OXFORD

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Gallus gallus domesticus

characteristic: host scientific name

text: Campylobacter

characteristic: isolate

text: Faeces

text: uncultured Campylobacter sp.

text: Faecal sample


E-MTAB-10756:Sample 12

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10756:Sample 12

tag: Namespace:KING'S COLLEGE LONDON

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: CD4-positive, CD25-positive, alpha-beta regulatory T cell

text: human

characteristic: common name

text: Protocols: Cryopreserved PBMC samples (10^6 cells) from baseline (1 or 2 weeks before first treatment) and 24 weeks post treatment timepoint were thawed from 10 subjects and stained first using live/dead violet then surface stained using CD14 CD3 CD4 CD25 CD127 antibodies. A minimum of 40,000 CD14- CD3+ CD4+ CD25+ CD127lo Tregs (average = 81,600, max = 158,300) were sorted using BD FACSAria III and frozen at -80C in minimal PBS prior to DNA/RNA extraction. DNA/RNA was extracted in parallel with the AllPrep micro kit (Qiagen) RNAseq libraries prepared from 2/3 of extracted RNA (91-140 ng) with SMART-Seq v4 and NuGen Ovation Ultralow

characteristic: description

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: male

characteristic: sex

text: Sample 12


E-MTAB-10756:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10756:Sample 14

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: female

text: Sample 14

characteristic: title


E-MTAB-10756:Sample 16

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10756:Sample 16

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 16


E-MTAB-10756:Sample 18

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 18

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

characteristic: sex

text: Sample 18


E-MTAB-10756:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

text: public

text: E-MTAB-10756:Sample 2

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 2


E-MTAB-10756:Sample 20

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10756:Sample 20

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: male

text: Sample 20

characteristic: title


E-MTAB-10756:Sample 4

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

characteristic: SRA accession

text: E-MTAB-10756:Sample 4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: autoimmune type 1 diabetes

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 4


E-MTAB-10756:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 6

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: male

characteristic: sex

text: Sample 6


E-MTAB-10756:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10756:Sample 8

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 8


E-MTAB-10756:Sample 9

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10756:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: female

text: Sample 9

characteristic: title


E-MTAB-10756:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 1

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: autoimmune type 1 diabetes

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 1


E-MTAB-10756:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 10

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

characteristic: sex

text: Sample 10


E-MTAB-10756:Sample 11

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10756:Sample 11

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: male

text: Sample 11


E-MTAB-10756:Sample 13

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: female

text: Sample 13

characteristic: title


E-MTAB-10756:Sample 15

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 15

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: autoimmune type 1 diabetes

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 15


E-MTAB-10756:Sample 17

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

text: public

text: E-MTAB-10756:Sample 17

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

characteristic: sex

text: Sample 17


E-MTAB-10756:Sample 19

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10756:Sample 19

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: male

text: Sample 19


E-MTAB-10756:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: autoimmune type 1 diabetes

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: female

text: Sample 3

characteristic: title


E-MTAB-10756:Sample 7

text: KING'S COLLEGE LONDON

characteristic: INSDC center alias

text: KING'S COLLEGE LONDON

characteristic: INSDC center name

text: public

text: E-MTAB-10756:Sample 7

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: adult

text: autoimmune type 1 diabetes

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: female

text: Sample 7


E-MTAB-10756:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KING'S COLLEGE LONDON

text: KING'S COLLEGE LONDON

text: public

text: E-MTAB-10756:Sample 5

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: autoimmune type 1 diabetes

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: male

characteristic: sex

text: Sample 5