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text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 8043, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 8051, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 8051, Visit 26w

characteristic: title

characteristic: visit


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 8075, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 8075, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 8082, Visit 4w

characteristic: title

characteristic: visit


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 8082, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 8083, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 8083, Visit 26w

characteristic: title

characteristic: visit


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 8087, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 8087, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 8089, Visit 4w

characteristic: title

characteristic: visit


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 8089, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 9002, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 9002, Visit 26w

characteristic: title

characteristic: visit


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 9004, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 9004, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 9019, Visit 4w

characteristic: title

characteristic: visit


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 9019, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 9024, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 9024, Visit 26w

characteristic: title

characteristic: visit


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

text: Singapore

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

characteristic: investigation type

text: Homo sapiens

characteristic: project name

text: Homo sapiens

text: Pyrosequencing

characteristic: sequencing method

text: Subject 4288, Visit 4w


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Nutricia Research

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: Homo sapiens

characteristic: environment (biome)

text: intestine environment

characteristic: environment (feature)

text: feces

text: Australia

text: human-gut

text: metagenome

text: Homo sapiens

text: Homo sapiens

text: Pyrosequencing

text: Subject 5020, Visit 26w


characteristic: External Id

text: Nutricia Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: intestine environment

text: feces

characteristic: environment (material)

text: Australia

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Pyrosequencing

text: Subject 5039, Visit 26w

characteristic: title

characteristic: visit


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

tag: Namespace:WAGENINGEN UNIVERSITY

text: Pseudovibrio sp. 1F12

text: Pseudovibrio sp. 1F12

text: Pseudovibrio sp. 1F12


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Pseudovibrio sp. 2G02

text: Pseudovibrio sp. 2G02

text: Pseudovibrio sp. 2G02


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 2G05

text: Pseudovibrio sp. 2G05

text: Pseudovibrio sp. 2G05


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 2H03

text: Pseudovibrio sp. 2H03

text: Pseudovibrio sp. 2H03


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 2H05

text: Pseudovibrio sp. 2H05

text: Pseudovibrio sp. 2H05


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 2H06

text: Pseudovibrio sp. 2H06

text: Pseudovibrio sp. 2H06


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 3C10

text: Pseudovibrio sp. 3C10

text: Pseudovibrio sp. 3C10


text: CGR

text: public

text: metagenome

text: metagenome

text: Viral metatranscriptome sample


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

characteristic: common name

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with narasin


characteristic: External Id

text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with no additive


text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC center name

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product A


text: NORWEGIAN VETERINARY INSTITUTE

characteristic: INSDC first public

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product B


text: NORWEGIAN VETERINARY INSTITUTE

text: public

characteristic: INSDC status

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product C


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product D


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product E


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product F


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with yeast product A


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with plant/acid product A


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with acid product B+synbiotic A


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with yeast product B+plant product A


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with yeast product A+acid product B


text: NORWEGIAN VETERINARY INSTITUTE

text: public

text: chicken

text: Gallus gallus

text: Gallus gallus

text: Caecal content of chickens fed a diet supplemented with yeast product A+acid product D


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 4H03

text: Pseudovibrio sp. 4H03

text: Pseudovibrio sp. 4H03


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 4H10

text: Pseudovibrio sp. 4H10

text: Pseudovibrio sp. 4H10


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 7A08

text: Pseudovibrio sp. 7A08

text: Pseudovibrio sp. 7A08


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 7F08

text: Pseudovibrio sp. 7F08

text: Pseudovibrio sp. 7F08


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 7G12

text: Pseudovibrio sp. 7G12

text: Pseudovibrio sp. 7G12


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 7H02

text: Pseudovibrio sp. 7H02

text: Pseudovibrio sp. 7H02


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 8G08

text: Pseudovibrio sp. 8G08

text: Pseudovibrio sp. 8G08


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 8H04

text: Pseudovibrio sp. 8H04

text: Pseudovibrio sp. 8H04


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 8H06

text: Pseudovibrio sp. 8H06

text: Pseudovibrio sp. 8H06


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. AB108

text: Pseudovibrio sp. AB108

text: Pseudovibrio sp. AB108


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. AB111

text: Pseudovibrio sp. AB111

text: Pseudovibrio sp. AB111


text: unspecified

text: public

text: 10 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Protocols: Mice were housed in an enhanced barrier specific pathogen-free facility under a strict 12-hour light cycle and fed irradiated chow diet (PicoLab Rodent Chow 20, Purina Mills). Mice were maintained on a C57BL/6 background. A heterozygous x heterozygous breeding scheme was used to generate Atg16l1 T300A and wildtype littermate control mice. All study protocols were approved by the Washington University Animal Studies Committee. Four- to six-week-old mice were exposed to mainstream cigarette smoking 4 cigarettes/day, 5 days/week, for 6 weeks, using Kentucky research cigarette 3R4F in a smoking chamber. All mice were sacrificed after completing 6 weeks of smoking exposure, and fecal samples were frozen down at the time of collection. DNA was isolated using Qiagen QIAmp DNA Stool Kit, according to the kit protocol. Total DNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. 14 PCR amplicons, representing all 9 16S variable regions, were constructed using the Fluidigm Access Array System. 5ng/ul of DNA were input into each reaction. The sample inlets consisted of 1X High Fidelity FastStart Reaction Buffer without MgCl2 (Roche), 4.5nM MgCl2 (Roche), 5% DMSO (Roche), 200uM PCR Grade Nucleotide Mix (Roche), 0.05 U/μL 5 U/μL FastStart High Fidelity Enzyme Blend (Roche), 1X Access Array Loading Reagent (Fluidigm), 1ul DNA, and water. The primers were added to the assay inlets at 200nM forward and reverse primers with 1X Access Array Loading Reagent. The samples were harvested after PCR amplification was performed on the BioMark HD system from Fluidigm. Each sample was harvested and indexed using unique 10 base pair sequences with 14 rounds of PCR to incorporate each index sequence. All samples were pooled into 48 sample libraries and cleaned using bead purification.

characteristic: description

text: non-smoking

characteristic: environmental history

text: Atg16l1 T300A

characteristic: genotype

text: Mus musculus

characteristic: host organism

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

characteristic: organism part

text: mouse gut metagenome

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: unspecified

characteristic: INSDC last update

text: public

text: 10 to 12

text: ArrayExpress

text: non-smoking

text: wild type genotype

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female

characteristic: title


characteristic: External Id

text: unspecified

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 10 to 12

text: ArrayExpress

text: non-smoking

text: wild type genotype

text: Mus musculus

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: male


text: unspecified

text: public

characteristic: INSDC status

text: 10 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

characteristic: description

text: smoking

characteristic: environmental history

text: Atg16l1 T300A

text: Mus musculus

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female


text: unspecified

text: public

text: 10 to 12

text: ArrayExpress

text: smoking

text: Atg16l1 T300A

characteristic: genotype

text: Mus musculus

characteristic: host organism

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

characteristic: organism part

text: mouse gut metagenome

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: unspecified

characteristic: INSDC last update

text: public

text: 10 to 12

text: ArrayExpress

text: smoking

text: wild type genotype

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female


characteristic: External Id

text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Pseudovibrio sp. AB113

text: Pseudovibrio sp. AB113

text: Pseudovibrio sp. AB113

characteristic: title


text: unspecified

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: Mice were housed in an enhanced barrier specific pathogen-free facility under a strict 12-hour light cycle and fed irradiated chow diet (PicoLab Rodent Chow 20, Purina Mills). Mice were maintained on a C57BL/6 background. A heterozygous x heterozygous breeding scheme was used to generate Atg16l1 T300A and wildtype littermate control mice. All study protocols were approved by the Washington University Animal Studies Committee. A set of 4- to 6-week-old Atg16l1 T300A and littermate mice were exposed to mainstream cigarette smoking 4 cigarettes/day, 5 days/week, for 2 weeks, using Kentucky research cigarette 3R4F in a smoking chamber. These mice were used as microbiota donors. A separate set of similar aged mice that were not exposed to cigarette smoking was used as microbiota recipients. The microbiota recipients were pre-treated with broad spectrum antibiotics (vancomycin, neomycin, ampicillin, and metronidazole) for a week prior to cohousing to eradicate existing commensal microbiota. The microbiota recipients were co-housed with microbiota donors of the same genotype for 4 weeks, during this period the donors continued to be exposed to cigarette smoking. All mice were sacrificed after being cohoused for 4 weeks, and fecal samples were frozen down at the time of collection. DNA was isolated using Qiagen QIAmp DNA Stool Kit, according to the kit protocol. Total DNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. 14 PCR amplicons, representing all 9 16S variable regions, were constructed using the Fluidigm Access Array System. 5ng/ul of DNA were input into each reaction. The sample inlets consisted of 1X High Fidelity FastStart Reaction Buffer without MgCl2 (Roche), 4.5nM MgCl2 (Roche), 5% DMSO (Roche), 200uM PCR Grade Nucleotide Mix (Roche), 0.05 U/μL 5 U/μL FastStart High Fidelity Enzyme Blend (Roche), 1X Access Array Loading Reagent (Fluidigm), 1ul DNA, and water. The primers were added to the assay inlets at 200nM forward and reverse primers with 1X Access Array Loading Reagent. The samples were harvested after PCR amplification was performed on the BioMark HD system from Fluidigm. Each sample was harvested and indexed using unique 10 base pair sequences with 14 rounds of PCR to incorporate each index sequence. All samples were pooled into 48 sample libraries and cleaned using bead purification.

characteristic: description

text: non-smoking, co-housed with smoking mice

text: Atg16l1 T300A

text: Mus musculus

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female


text: unspecified

text: public

text: ArrayExpress

text: smoking

characteristic: environmental history

text: Atg16l1 T300A

characteristic: genotype

text: Mus musculus

characteristic: host organism

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

characteristic: organism part

text: mouse gut metagenome

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: unspecified

text: public

text: ArrayExpress

text: wild type genotype

text: Mus musculus

text: mouse gut metagenome

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: unspecified

characteristic: INSDC last update

text: public

text: ArrayExpress

text: smoking

text: wild type genotype

text: Mus musculus

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: feces

text: mouse gut metagenome

text: female


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Pseudovibrio sp. BC118

text: Pseudovibrio sp. BC118

text: Pseudovibrio sp. BC118

characteristic: title


text: WAGENINGEN UNIVERSITY

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: Pseudovibrio ascidiaceicola

text: Pseudovibrio ascidiaceicola

text: Pseudovibrio ascidiaceicola


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio axinellae

text: Pseudovibrio axinellae

text: Pseudovibrio axinellae


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio denitrificans JCM 12308

text: Pseudovibrio denitrificans JCM 12308

text: Pseudovibrio denitrificans JCM 12308


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio japonicus

text: Pseudovibrio japonicus

text: Pseudovibrio japonicus


text: Universita degli studi di Ferrara

text: public

tag: Namespace:Universita degli studi di Ferrara

text: human

characteristic: common name

text: Mesolithic human sample from Romania (Schela Cladovei)

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: Universita degli studi di Ferrara

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Ancient human

type: has member


text: Universita degli studi di Ferrara

text: public

text: human

text: Mesolithic human sample from Romania (Ostrovul Corbului)

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: Universita degli studi di Ferrara

text: public

text: human

text: Mesolithic human sample from Spain (Gura Baciului)

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: Universita degli studi di Ferrara

text: public

text: human

text: Mesolithic human sample from Spain (Chan do Lindeiro)

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: Universita degli studi di Ferrara

text: public

text: human

text: Mesolithic human sample from Spain (Canes)

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: Universita degli studi di Ferrara

text: public

text: human

text: Ancient human sample

text: Homo sapiens

text: Homo sapiens

text: Ancient human


text: WAGENINGEN UNIVERSITY

text: public

text: Pseudovibrio sp. 7H04

text: Pseudovibrio sp. 7H04

text: Pseudovibrio sp. 7H04


text: WUR

text: public

characteristic: collection date

text: granular sludge

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Co

characteristic: metal

text: 30 mM

characteristic: metal concentration

text: metagenome

text: Supplemented with 45 mM of SO4

characteristic: others

text: Effect of nickel and cobalt on methanogenic enrichment cultures and role of biogenic sulphide in metal toxicity attenuation

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Acetate

characteristic: substrate

text: Sample supplemented with 30 mM of Co and 45 mM of SO4 using acetate as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: Co

text: 30 mM

text: metagenome

characteristic: organism

text: Supplemented with 30 mM of H2S

text: metagenome

text: Illumina MiSeq

text: Acetate

text: Sample supplemented with 30 mM of Co and 30 mM of H2S using acetate as substrate

characteristic: title

text: wastewater/sludge


text: WUR

text: public

characteristic: collection date

text: granular sludge

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Ni

characteristic: metal

text: 8 mM

characteristic: metal concentration

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Acetate

text: Sample supplemented with 8 mM of Ni using acetate as substrate

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: Ni

text: 4 µM

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Acetate

characteristic: substrate

text: Sample supplemented with 4 µM of Ni using acetate as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WUR

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

text: metagenome

text: Co

text: 10 µM

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Acetate

text: Sample supplemented with 10 µM of Co using acetate as substrate

characteristic: title

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

text: public

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: No metal supplementation

characteristic: metal

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample without metal supplementation using hydrogen as substrate

text: wastewater/sludge


text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: No metal supplementation

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Acetate

characteristic: substrate

text: Sample without metal supplementation using acetate as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

text: metagenome

text: Ni

text: 4 µM

characteristic: metal concentration

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample supplemented with 4 µM of Ni using hydrogen as substrate

characteristic: title

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Ni

characteristic: metal

text: 8 mM

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample supplemented with 8 mM of Ni using hydrogen as substrate

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: Ni

text: 8 mM

text: metagenome

text: Supplemented with 8 mM of SO4

characteristic: others

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Hydrogen

characteristic: substrate

text: Sample supplemented with 8 mM of Ni and 8 mM of SO4 using hydrogen as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: granular sludge

characteristic: environment (biome)

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

text: metagenome

text: Ni

text: 8 mM

characteristic: metal concentration

text: metagenome

characteristic: organism

text: Supplemented with 8 mM of H2S

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample supplemented with 8 mM of Ni and 8 mM of H2S using hydrogen as substrate

characteristic: title

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Ni

characteristic: metal

text: 8 mM

text: metagenome

text: Supplemented with 8 mM of SO4

text: metagenome

text: Illumina MiSeq

text: Acetate

text: Sample supplemented with 8 mM of Ni and 8 mM of SO4 using acetate as substrate

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: granular sludge

characteristic: environment (biome)

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: Ni

text: 8 mM

text: metagenome

text: Supplemented with 8 mM of H2S

characteristic: others

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Acetate

characteristic: substrate

text: Sample supplemented with 8 mM of Ni and 8 mM of H2S using acetate as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

text: metagenome

text: Co

text: 10 µM

characteristic: metal concentration

text: metagenome

characteristic: organism

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample supplemented with 10 µM of Co using hydrogen as substrate

characteristic: title

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: granular sludge

characteristic: environment (biome)

text: anaerobic

text: wastewater

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Co

characteristic: metal

text: 30 mM

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Acetate

text: Sample supplemented with 30 mM of Co using acetate as substrate

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: granular sludge

text: anaerobic

text: wastewater

text: Netherlands

text: metagenome

text: Co

text: 30 mM

text: metagenome

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Hydrogen

characteristic: substrate

text: Sample supplemented with 30 mM of Co using hydrogen as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: granular sludge

text: anaerobic

characteristic: environment (feature)

text: wastewater

characteristic: environment (material)

text: Netherlands

text: metagenome

text: Co

text: 30 mM

characteristic: metal concentration

text: metagenome

characteristic: organism

text: supplemented with 45 mM SO4

characteristic: others

text: Effect of nickel and cobalt on methanogenic enrichment cultures and role of biogenic sulphide in metal toxicity attenuation

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: Sample supplemented with 30 mM of Co and 45 mM of SO4 using hydrogen as substrate

characteristic: title

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WUR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: granular sludge

characteristic: environment (biome)

text: anaerobic

text: wastewater

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Co

characteristic: metal

text: 30 mM

text: metagenome

text: Supplemented with 45 mM SO4

text: metagenome

text: Illumina MiSeq

text: Hydrogen

text: wastewater/sludge


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: granular sludge

text: anaerobic

characteristic: environment (feature)

text: wastewater

text: Netherlands

text: metagenome

text: Co

text: 30 mM

text: metagenome

text: Supplemented with 30 mM of H2S

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: Hydrogen

characteristic: substrate

text: Sample supplemented with 30 mM of Co and 30 mM of H2S using hydrogen as substrate

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: KAIST

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Medical University of Graz

text: public

tag: Namespace:Medical University of Graz

text: Nasal microbiome

characteristic: environment (biome)

text: Olfactory mucosal microbiome

text: Olfactory mucosa

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: human metagenome

text: The nasal microbiome mirrors and potentially shapes olfactory function

text: human metagenome

text: Illumina MiSeq

text: Nasal microbiome


text: LIV

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Indianmeal moth

characteristic: common name

text: Plodia interpunctella

text: Plodia interpunctella

text: Female

characteristic: sex

text: Dundee

characteristic: strain

text: Plodia interpunctella inbred line


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Geogentics

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Staphylococcus argenteus

text: Staphylococcus argenteus in Denmark

characteristic: description

text: Denmark

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Soft-skin infection or carrier

characteristic: isolation source

text: Staphylococcus argenteus

characteristic: organism

text: Staphylococcus argenteus

characteristic: unique name


text: Salmonella enterica subsp. enterica serovar Typhimurium

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: subject id

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: COD

characteristic: common name

text: Salmonella

characteristic: genus

text: Homo sapiens

characteristic: host

type: AMR curated data - CABBAGE

value: azithromycin

value: e-test

value: mg/L

value: Salmonella enterica

value: ceftazidime-clavulanic acid

value: CLSI

value: disk diffusion

value: susceptible

value: meropenem

value: pefloxacin

value: ceftriaxone

value: resistant

value: ertapenem

value: trimethoprim-sulfamethoxazole

value: nalidixic acid

value: tetracycline

value: cefotaxime

value: ampicillin

value: chloramphenicol

value: ceftazidime

value: gentamicin

value: cefotaxime-clavulanic acid


text: SC

text: public

text: COD

characteristic: SRA accession

characteristic: Submitter Id

text: Salmonella

text: Homo sapiens

characteristic: isolate

value: CLSI

value: Salmonella enterica

value: ceftazidime-clavulanic acid

value: azithromycin

value: e-test

value: mg/L


characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: organism

value: disk diffusion

value: susceptible

value: pefloxacin

value: resistant

value: ceftriaxone

value: meropenem


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: nalidixic acid

value: trimethoprim-sulfamethoxazole

value: tetracycline

value: ampicillin

value: cefotaxime

value: ertapenem


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: CLSI

value: Salmonella enterica

value: cefotaxime-clavulanic acid

value: ceftazidime

value: gentamicin

value: chloramphenicol


text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: subject id

characteristic: title

value: disk diffusion

value: susceptible

value: azithromycin

value: e-test

value: mg/L

value: ceftazidime-clavulanic acid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: ceftriaxone

value: resistant

value: trimethoprim-sulfamethoxazole

value: pefloxacin

value: meropenem

value: nalidixic acid


text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: COD

text: Salmonella

text: Homo sapiens

value: ampicillin

value: CLSI

value: Salmonella enterica

value: ertapenem

value: cefotaxime

value: tetracycline


text: SC

text: public

text: COD

characteristic: common name

text: Salmonella

characteristic: genus

text: Homo sapiens

value: disk diffusion

value: susceptible

value: gentamicin

value: cefotaxime-clavulanic acid

value: ceftazidime

value: chloramphenicol


text: SC

text: public

text: COD

characteristic: SRA accession

text: Salmonella

text: Homo sapiens

characteristic: host

value: resistant

value: azithromycin

value: e-test

value: mg/L

value: ceftriaxone

value: ceftazidime-clavulanic acid


text: SC

text: public

text: COD

characteristic: Submitter Id

text: Salmonella

text: Homo sapiens

characteristic: isolate

value: pefloxacin

value: CLSI

value: nalidixic acid

value: ampicillin

value: trimethoprim-sulfamethoxazole

value: meropenem


characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: organism

value: disk diffusion

value: susceptible

value: Salmonella enterica

value: ertapenem

value: cefotaxime

value: tetracycline


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: chloramphenicol

value: resistant

value: ceftazidime

value: cefotaxime-clavulanic acid

value: gentamicin

value: azithromycin


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: ceftriaxone

value: CLSI

value: e-test

value: mg/L

value: pefloxacin

value: ceftazidime-clavulanic acid


text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: subject id

characteristic: title

value: meropenem

value: disk diffusion

value: susceptible

value: ampicillin

value: trimethoprim-sulfamethoxazole

value: nalidixic acid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: Salmonella enterica

value: tetracycline

value: resistant

value: cefotaxime

value: chloramphenicol

value: ertapenem


text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status


text: SC

text: public

text: COD

characteristic: common name

text: Salmonella

characteristic: genus

text: Homo sapiens

value: CLSI

value: ceftazidime

value: gentamicin

value: cefotaxime-clavulanic acid

value: azithromycin

value: ceftriaxone


text: SC

text: public

text: COD

characteristic: SRA accession

text: Salmonella

text: Homo sapiens

characteristic: host

value: ceftazidime-clavulanic acid

value: disk diffusion

value: e-test

value: mg/L

value: pefloxacin

value: meropenem


text: SC

text: public

text: COD

characteristic: Submitter Id

text: Salmonella

text: Homo sapiens

characteristic: isolate

value: susceptible

value: Salmonella enterica

value: ampicillin

value: trimethoprim-sulfamethoxazole

value: nalidixic acid

value: tetracycline


characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: organism

value: ceftazidime

value: CLSI

value: cefotaxime

value: resistant

value: ertapenem

value: chloramphenicol


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: disk diffusion

value: ceftriaxone

value: ceftazidime-clavulanic acid

value: gentamicin

value: cefotaxime-clavulanic acid

value: azithromycin


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: Salmonella enterica

value: e-test

value: mg/L

value: susceptible

value: meropenem

value: pefloxacin


text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

characteristic: subject id

characteristic: title

value: trimethoprim-sulfamethoxazole

value: CLSI

value: ampicillin

value: tetracycline

value: ceftazidime

value: nalidixic acid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: COD

text: Salmonella

text: Homo sapiens

value: disk diffusion

value: ceftriaxone

value: resistant

value: chloramphenicol

value: ertapenem

value: cefotaxime


text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: COD

text: Salmonella

text: Homo sapiens

value: Salmonella enterica

value: azithromycin

value: e-test

value: gentamicin

value: ceftazidime-clavulanic acid

value: cefotaxime-clavulanic acid


text: Streptococcus pneumoniae

text: SC

text: public

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus

characteristic: genus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

value: susceptible

value: Streptococcus pneumoniae

value: penicillin

value: erythromycin


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: host

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

value: tetracycline


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: isolate

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

characteristic: INSDC first public

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


text: Streptococcus pneumoniae

characteristic: ENA-CHECKLIST

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: title


text: Streptococcus pneumoniae

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

characteristic: INSDC status

text: NLD

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus

characteristic: genus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: host

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: isolate

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

characteristic: INSDC first public

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


text: Streptococcus pneumoniae

characteristic: ENA-CHECKLIST

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: title


text: Streptococcus pneumoniae

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

characteristic: INSDC status

text: NLD

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus

characteristic: genus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: host

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

characteristic: isolate

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

characteristic: INSDC first public

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


text: Streptococcus pneumoniae

characteristic: ENA-CHECKLIST

text: SC

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: title


text: Streptococcus pneumoniae

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: NLD

text: Streptococcus pneumoniae

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

characteristic: INSDC status

text: NLD

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

text: NLD

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus

characteristic: genus

text: Homo sapiens

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


E-MTAB-5692:Sample 1

text: unspecified

text: public

text: E-MTAB-5692:Sample 1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T-helper 17 cell

characteristic: cell type

text: house mouse

text: Protocols: For T cell differentiation in vitro, spleens as well as brachial, axial, inguinal and mesenteric lymph nodes were isolated and separated into single cells. Viable lymphocytes were then separated from the remaining cells in Lympholyte-M Cell Separation medium (Cedarlane # CL5030) during a 15 min centrifugation step at 1250 g. Naive CD4+ CD62L+ T cells were obtained using Milteny’s CD4+CD62 L+ T Cell Isolation Kit II (#130-093-227) following the manufacturer’s instructions. Cells were cultured in IMDM supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 200 µM 2-ME, and 5 % FBS. Th17, For conventional Th17 cell differentiation, T cells were cultured in the presence of 25 ng/ml IL-6 (PeproTech #AF-200-06), 0.4 ng/ml TGFβ (PeproTech #100-21) and 4 μg/ml anti-IFN-γ antibodies (BioXCell Clone XMG1.2) for 3 days. ER stress-generated Th17 cells were obtained by a combined treatment of 25 ng/ml IL-6, and 4 μg/ml anti-IFN-γ antibodies with 2uM CPA (cyclopiazonic acid; Sigma # C1530) for 3 days. In vitro-differentiated Th17 cells obtained from IL-17ACre Rosastop-tdRFP were used for FACS. After 3 days of culture in 24-well plates, T cells were washed once with PBS and stained with APC-coupled anti-CD4 antibodies and DAPI (Molecular Probes #D1306) as a live/dead stain. CD4+ DAPI- cells were sorted according to their FP expression levels by a BD FACSAria. Samples for RNA sequencing were stored in 40 μl RNAlater at -80°C. RNA isolation was performed using Qiagen’s RNeasy Mini Plus Kit (#74134) following the manufacturer’s instructions. The RNA Integrity Number (RIN) was determined by running the samples on a Agilent Bioanalyser RNA Pico Chip (#5067- 1513). The RNA content was determined on a NanoDrop spectrometer and ranged from 0.9 - 11.1 μg RNA per sample. Two samples per experiment were chosen for RNA sequencing based on their RIN. An input of 250 ng RNA per sample was used for the subsequent generation of undirectional RNA libraries using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (#E7530S), following the manufacturer’s instructions (Figure 3). Succeeding an rRNA depletion step performed with the NEBNext® rRNA Depletion Kit (#E6310), we fragmented the RNA for 15min at 94°C to obtain RNA fragments about 200 bp in size. After adapter ligation, we used NEBNext Multiplex Oligos for Illumina (Set 1, NEB #E7335) to generate barcoded samples for multiplexing. PCR library enrichment was performed for 13 cycles. The quality of RNA libraries was assessed on Agilent Bioanalyser High Sensitivity DNA Chips (#5067-4626).

characteristic: description

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

characteristic: genotype

text: 25 ng/ml IL-6, 0.4 ng/ml TGF and 4 g/ml antiIFN- antibodies

characteristic: growth condition

text: IL17-Cre Rosa-RFP 13.2f

characteristic: individual

text: Mus musculus

text: Mus musculus

text: RFP positive

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-5692:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: unspecified

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5692:Sample 3

text: ArrayExpress

text: T-helper 17 cell

text: house mouse

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

text: IL17-Cre Rosa-RFP 19.2b

text: Mus musculus

characteristic: organism

text: Mus musculus

text: RFP positive

text: Mus musculus

text: male

text: Sample 3

characteristic: title


E-MTAB-5692:Sample 5

text: unspecified

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5692:Sample 5

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: T-helper 17 cell

text: house mouse

characteristic: common name

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

text: IL17-Cre Rosa-RFP M00183891

text: Mus musculus

text: Mus musculus

text: RFP positive

text: Mus musculus

text: male

text: Sample 5


E-MTAB-5692:Sample 7

text: unspecified

text: public

text: E-MTAB-5692:Sample 7

text: ArrayExpress

text: T-helper 17 cell

characteristic: cell type

text: house mouse

characteristic: description

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

characteristic: genotype

characteristic: growth condition

text: IL17-Cre Rosa-RFP M00183889

characteristic: individual

text: Mus musculus

text: Mus musculus

text: RFP positive

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

text: Sample 7


E-MTAB-5692:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: unspecified

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5692:Sample 2

text: ArrayExpress

text: T-helper 17 cell

text: house mouse

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

text: 25 ng/ml IL-6, 2uM CPA and 4 g/ml antiIFN- antibodies

text: IL17-Cre Rosa-RFP 13.2f

text: Mus musculus

text: Mus musculus

text: RFP positive

text: Mus musculus

text: male

characteristic: strain

text: Sample 2


E-MTAB-5692:Sample 4

text: unspecified

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5692:Sample 4

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: T-helper 17 cell

text: house mouse

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

text: IL17-Cre Rosa-RFP 19.2b

text: Mus musculus

characteristic: organism

text: Mus musculus

text: RFP positive

text: Mus musculus

text: male

text: Sample 4

characteristic: title


E-MTAB-5692:Sample 6

text: unspecified

text: public

text: E-MTAB-5692:Sample 6

text: ArrayExpress

characteristic: broker name

text: T-helper 17 cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

characteristic: genotype

characteristic: growth condition

text: IL17-Cre Rosa-RFP M00183891

characteristic: individual

text: Mus musculus

text: Mus musculus

text: RFP positive

text: Mus musculus

text: male

text: Sample 6


E-MTAB-5692:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: unspecified

characteristic: INSDC center name

text: public

text: E-MTAB-5692:Sample 8

text: ArrayExpress

text: T-helper 17 cell

text: house mouse

text: Il17atm1.1Stck-Cre Gt(ROSA)26SortdRFP

text: IL17-Cre Rosa-RFP M00183889

text: Mus musculus

text: Mus musculus

text: RFP positive

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

text: Sample 8


Magnetospirillum sp. strain 15-1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Magnetospirillum sp. strain 15-1

tag: Namespace:HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ

characteristic: Submitter Id

text: Vanessa Luensmann, Ingrid Meyer-Cifuentes

characteristic: collected by

characteristic: collection date

text: Germany

characteristic: geographic location (country and/or sea)

text: Saxony, Leipzig

characteristic: geographic location (region and locality)

text: Ingrid Meyer-Cifuentes

characteristic: identified by

text: Planted Fixed-bed Reactor

characteristic: isolation source

text: Magnetospirillum sp. 15-1

text: Magnetospirillum sp. 15-1

characteristic: strain

text: Draft Genome Sequence of Magnetospirillum sp. strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-bed Reactor.


text: Plasmodium malariae

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Plasmodium malariae

characteristic: common name

text: Plasmodium malariae

characteristic: organism

text: Plasmodium malariae

characteristic: subject id

characteristic: title


text: Streptococcus pneumoniae

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: TRINITY COLLEGE DUBLIN

text: public

tag: Namespace:TRINITY COLLEGE DUBLIN

characteristic: Submitter Id

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Human

characteristic: host scientific name

text: MTBC Culture Isolate

characteristic: isolate

text: Human

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: MTBC Culture Isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IPK-Gatersleben

text: public

text: Hordeum bulbosum accession FB2012-011-2 (FBB)

characteristic: description

text: Hordeum bulbosum

text: Hordeum bulbosum

text: HORBU WGS


text: Institute for Research in Biomedicine

text: public

tag: Namespace:Institute for Research in Biomedicine

text: metagenome

characteristic: organism

text: metagenome

text: IgA-targeted gut microbiota

characteristic: title