characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Dept. of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU)

unit: day

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: RNA was extracted (see nucleic acid extraction protocol) from small intestinal organoids (see growth protocol) treated with cytokines for different time points (see treatment protocol), a library was created (see nucleic acid library construction protocol) and sequenced paired end 150 bp (see nucleic acid sequencing protocol) Crypts from small intestine were isolated according to a published protocol (Sato 2013). In summary, the small intestine of mouse was washed in ice-cold PBS and opened longitudinally. A microscopy cover slip was used to gently scrape of excess mucus and villus before the intestine was cut into 2-4 mm pieces. The fragments were resuspended in 30 mL ice-cold PBS and pipetted up and down with a 10 mL pipette. Supernatant was discarded and this step was repeated 5-10 times until the supernatant was clear. The fragments were incubated in 2 mM EDTA in PBS for small intestine at 4 C for 30 min with gentle rocking. The supernatant was removed, 20 mL of ice-cold PBS was added and the fragments were pipetted up and down. This washing step was repeated until the crypt fraction appeared as seen in a microscope. The 1-3 consecutive crypt fractions were passed through a 70 um cell strainer and collected into a FCS coated 50 mL tube. The crypts were spun down at 300 xg for 5 min and washed once in 10 mL ice cold PBS at 200 xg for 5 min. Approximately 200-500 crypts were resuspended in 50 uL Matrigel and kept at 4 C. 50 uL of the matrigel solution were added to the center of a pre-warmed 24 well plate and quickly transferred to an incubator at 37 degrees with 5 % CO2. After 5 min the pellet had solidified and 500 uL of basal culture medium was added and the plate was put back into the incubator. Basal culture medium consisted of advanced Dulbecco's modified Eagle medium - F12 supplemented with penicillin/streptomycin, 10 mM HEPES, 2 mM Glutamax, 1x N2 [ThermoFisher Scientific 100X, 17502048], 1x B-27 [ThermoFisher Scientific 50X, 17504044], and 1x N-acetyl-L-cysteine [Sigma, A7250]) and overlaid with ENR factors containing 50 ng/ml of murine EGF [Thermo Fisher Scientific, PMG8041], 20 % condition medium (CM) from a cell line producing R-Spondin (kind gift from Calvin Kuo, Stanford University School of Medicine, Stanford, CA, USA) and 10 % Noggin-CM (a kind gift from Hans Clevers, Hubrecht Institute, Utrecht, The Netherlands). The culture medium was replaced every 2-3 days. Organoids were passaged by disrupting them with strong mechanical pipetting, letting the solution cool on ice before centrifuging at 200 xg, 5 min at 4 C and resuspending in matrigel. References:Sato, Toshiro and Hans Clevers (2013). “Primary Mouse Small Intestinal Epithelial Cell Cultures”. In:Epithelial Cell Culture Protocols: Second Edition. Ed. by Scott H. Randell and M. Leslie Fulcher. Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 319-328.isbn: 978-1-62703-125-7.doi:10.1007/978-1-62703-125-7_19.527url:https://doi.org/10.1007/978-1-62703-125-7_19. Intestinal organoids were split and seeded on a new plate and lysed after 48 hours of growth. 10 ng/mL of IL-22 (Peprotech #210-22) were applied to wells 1 hour and 4 hours hours before lysis. Three 24 well plate wells were combined together per sample for RNA extraction. RNA was extracted with Quick-RNA Microprep Kit according to the manufacturers instructions (Zymo, R1050). Library preparation was done with NEB Next(R) Ultra(TM) RNA Library Prep Kit

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

text: organoid culture

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epithelium of small intestine

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Dept. of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU)

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

characteristic: genotype

text: organoid culture

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epithelium of small intestine

characteristic: organism part

text: Mus musculus

text: female

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Centre for Translational Microbiome Research (CTMR)

characteristic: collection date

text: We collected fecal samples from children with therapy-resistant epilepsy before starting KD and after three months on the diet. Applying shotgun metagenomic DNA sequencing we established taxonomic profiles.

text: feces

characteristic: environment (biome)

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

text: not collected

unit: DD

characteristic: geographic location (latitude)

text: not collected

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human feces metagenome

characteristic: project name

text: human feces metagenome

text: shotgun metagenomic sequencing (Illumina)

characteristic: sequencing method

text: Metagenomic sequencing of fecal samples from children with drug-resistant epilepsy before and during keetogenic diet treatment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Translational Microbiome Research (CTMR)

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: description

text: feces

text: feces

text: feces

text: Sweden

text: not collected

text: not collected

text: human-gut

text: metagenome

text: human feces metagenome

characteristic: organism

text: human feces metagenome


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University of Ljubljana, Biotechnical faculty

text: not provided

characteristic: collection date

text: human milk sample

text: human

characteristic: environment (biome)

text: milk

characteristic: environment (feature)

text: human milk

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: human-associated

characteristic: human associated environmental package

text: Bifidobacterium animalis subsp. lactis

text: Resistomes of probiotic and starter cultures as potential risk factors for the spread of antibiotic resistance

text: Bifidobacterium animalis subsp. lactis

text: Illumina MiSeq v3

text: Bifidobacterium animalis subsp. lactis IM841

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Ljubljana, Biotechnical faculty

text: public

text: not provided

text: human milk sample

text: human

text: milk

text: human milk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: human-associated

characteristic: investigation type

text: Bifidobacterium breve

characteristic: project name

text: Bifidobacterium breve

text: Illumina MiSeq v3

characteristic: sequencing method

text: Bifidobacterium breve IM703


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: human milk sample

characteristic: description

text: human

text: milk

text: human milk

text: Slovenia

text: not provided

text: not provided

text: human-associated

text: Bifidobacterium longum subsp. longum

characteristic: organism

text: Bifidobacterium longum subsp. longum

text: Illumina MiSeq v3

text: Bifidobacterium longum subsp. longum IM937


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: human milk sample

text: human

characteristic: environment (biome)

text: milk

characteristic: environment (feature)

text: human milk

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: human-associated

characteristic: human associated environmental package

text: Illumina MiSeq v3

text: Lacticaseibacillus paracasei subsp. paracasei IM932

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: human milk sample

text: human

text: milk

text: human milk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: human-associated

characteristic: investigation type

text: Lactiplantibacillus plantarum

characteristic: project name

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactiplantibacillus plantarum IM930


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: human milk sample

characteristic: description

text: human

text: milk

text: human milk

text: Slovenia

text: not provided

text: not provided

text: human-associated

text: Lactobacillus paragasseri

characteristic: organism

text: Lactobacillus paragasseri

text: Illumina MiSeq v3

text: Lactobacillus paragasseri IM914


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: human milk sample

text: human

characteristic: environment (biome)

text: milk

characteristic: environment (feature)

text: human milk

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: human-associated

characteristic: human associated environmental package

text: Ligilactobacillus salivarius

text: Ligilactobacillus salivarius

text: Illumina MiSeq v3

text: Ligilactobacillus salivarius IM849

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: human milk sample

text: human

text: milk

text: human milk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: human-associated

characteristic: investigation type

text: Limosilactobacillus fermentum

characteristic: project name

text: Limosilactobacillus fermentum

text: Illumina MiSeq v3

characteristic: sequencing method

text: Limosilactobacillus fermentum IM863


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: human milk sample

characteristic: description

text: human

text: milk

text: human milk

text: Slovenia

text: not provided

text: not provided

text: human-associated

text: Limosilactobacillus reuteri

characteristic: organism

text: Limosilactobacillus reuteri

text: Illumina MiSeq v3

text: Limosilactobacillus reuteri IM842


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: human milk sample

text: human

characteristic: environment (biome)

text: milk

characteristic: environment (feature)

text: human milk

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: human-associated

characteristic: human associated environmental package

text: Limosilactobacillus vaginalis

text: Limosilactobacillus vaginalis

text: Illumina MiSeq v3

text: Limosilactobacillus vaginalis IM929

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: human milk sample

text: human

text: milk

text: human milk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: human-associated

characteristic: investigation type

text: Pediococcus acidilactici

characteristic: project name

text: Pediococcus acidilactici

text: Illumina MiSeq v3

characteristic: sequencing method

text: Pediococcus acidilactici IM716


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: cheese or cheese product

text: cheese with herbs

text: Slovenia

text: not provided

text: not provided

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: Enterococcus faecalis

characteristic: organism

text: Enterococcus faecalis

text: Illumina MiSeq v3

text: Enterococcus faecalis IM1301


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: milk or milk product

characteristic: environment (feature)

text: fermented goat butter

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Illumina MiSeq v3

text: Enterococcus faecalis IM1312

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: cheese form cow's milk, Zlatar

text: Serbia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Enterococcus faecalis

characteristic: project name

text: Enterococcus faecalis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Enterococcus faecalis IM1315


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: cheese or cheese product

text: traditional Serbian cheese

text: Serbia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Enterococcus faecalis

characteristic: organism

text: Enterococcus faecalis

text: Illumina MiSeq v3

text: Enterococcus faecalis IM1437


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: traditional Serbian cheese

characteristic: environment (material)

text: Serbia

text: not provided

text: not provided

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Illumina MiSeq v3

text: Enterococcus faecalis IM1438

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: traditional Slovenian cheese Mohant

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Enterococcus faecalis

characteristic: project name

text: Enterococcus faecalis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Enterococcus faecalis IM1305


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: cheese or cheese product

text: traditional Serbian cheese

text: Serbia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Enterococcus faecium

characteristic: organism

text: Enterococcus faecium

text: Illumina MiSeq v3

text: Enterococcus faecium IM1439


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: cheese Sremski

characteristic: environment (material)

text: Serbia

text: not provided

text: not provided

text: Enterococcus italicus

text: Enterococcus italicus

text: Illumina MiSeq v3

text: Enterococcus italicus IM1319

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: cheese form cow's milk, Sjenicki

text: Serbia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Enterococcus italicus

characteristic: project name

text: Enterococcus italicus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Enterococcus italicus IM1314


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: cheese or cheese product

text: cheese Edam

text: Slovenia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Enterococcus malodoratus

characteristic: organism

text: Enterococcus malodoratus

text: Illumina MiSeq v3

text: Enterococcus malodoratus IM1302


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: cheese form cow's milk, Sjenicki

characteristic: environment (material)

text: Serbia

text: not provided

text: not provided

text: Lactiplantibacillus paraplantarum

text: Lactiplantibacillus paraplantarum

text: Illumina MiSeq v3

text: Lactiplantibacillus paraplantarum IM1334

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: cheese Grana Padano

text: Italy

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lactiplantibacillus plantarum

characteristic: project name

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactiplantibacillus plantarum IM1130


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: cheese or cheese product

text: cheese Grana Padano

text: Italy

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lactiplantibacillus plantarum

characteristic: organism

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

text: Lactiplantibacillus plantarum IM1131


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: cheese Planinski

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Lactiplantibacillus plantarum

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

text: Lactiplantibacillus plantarum IM1155

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: milk or milk product

text: sour milk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lactococcus lactis subsp. lactis

characteristic: project name

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactococcus lactis subsp. lactis IM143


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: milk or milk product

text: sour milk

text: Slovenia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lactococcus lactis subsp. lactis

characteristic: organism

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

text: Lactococcus lactis subsp. lactis IM145


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: milk or milk product

characteristic: environment (feature)

text: fermented goat butter

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Lactococcus lactis subsp. lactis

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

text: Lactococcus lactis subsp. lactis IM1325

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: milk or milk product

text: fermented goat buttermilk

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lactococcus lactis subsp. lactis

characteristic: project name

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactococcus lactis subsp. lactis IM1326


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: milk or milk product

text: kefir

text: Russia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lentilactobacillus kefiri

characteristic: organism

text: Lentilactobacillus kefiri

text: Illumina MiSeq v3

text: Lentilactobacillus kefiri IM1365


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: goat cheese

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Leuconostoc citreum

text: Leuconostoc citreum

text: Illumina MiSeq v3

text: Leuconostoc citreum IM1329

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: traditional Slovenian cheese Mohant

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Levilactobacillus brevis

characteristic: project name

text: Levilactobacillus brevis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Levilactobacillus brevis IM1293


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: non-starter dairy isolate

characteristic: description

text: dairy product

text: milk or milk product

text: goat milk

text: Slovenia

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Levilactobacillus brevis

characteristic: organism

text: Levilactobacillus brevis

text: Illumina MiSeq v3

text: Levilactobacillus brevis IM1297


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: non-starter dairy isolate

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: cheese Planinski

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Pediococcus pentosaceus

text: Pediococcus pentosaceus

text: Illumina MiSeq v3

text: Pediococcus pentosaceus IM1147

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: non-starter dairy isolate

text: dairy product

text: cheese or cheese product

text: goat cheese

text: Slovenia

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Enterococcus faecium

characteristic: project name

text: Enterococcus faecium

text: Illumina MiSeq v3

characteristic: sequencing method

text: Enterococcus faecium IM1313


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: strain from feed additive

characteristic: description

text: feed

text: feed additive

text: feed additive Lactiferm

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Enterococcus faecium

characteristic: organism

text: Enterococcus faecium

text: Illumina MiSeq v3

text: Enterococcus faecium IM1478


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: strain from feed additive

text: feed

characteristic: environment (biome)

text: feed additive

characteristic: environment (feature)

text: feed additive Enterosan

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Limosilactobacillus reuteri

text: Limosilactobacillus reuteri

text: Illumina MiSeq v3

text: Limosilactobacillus reuteri IM110

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: strain from feed additive

text: feed

text: feed additive

text: feed additive Enterosan

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Pediococcus acidilactici

characteristic: project name

text: Pediococcus acidilactici

text: Illumina MiSeq v3

characteristic: sequencing method

text: Pediococcus acidilactici IM113


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Bio-Kult infantis

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Bifidobacterium breve

characteristic: organism

text: Bifidobacterium breve

text: Illumina MiSeq v3

text: Bifidobacterium breve IM1336


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: food additive Jamieson Probiotic 30 Billion

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Bifidobacterium breve

text: Bifidobacterium breve

text: Illumina MiSeq v3

text: Bifidobacterium breve IM1386

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: Linex

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Bifidobacterium longum subsp. infantis

characteristic: project name

text: Bifidobacterium longum subsp. infantis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Bifidobacterium longum subsp. infantis IM217


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Floractin

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Bifidobacterium longum subsp. longum

characteristic: organism

text: Bifidobacterium longum subsp. longum

text: Illumina MiSeq v3

text: Bifidobacterium longum subsp. longum IM810


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: Linex

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Enterococcus faecium

text: Enterococcus faecium

text: Illumina MiSeq v3

text: Enterococcus faecium IM215

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: food additive Waya AB

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Enterococcus faecium

characteristic: project name

text: Enterococcus faecium

text: Illumina MiSeq v3

characteristic: sequencing method

text: Enterococcus faecium IM578


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Bio-Kult infantis

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

characteristic: organism

text: Illumina MiSeq v3

text: Lacticaseibacillus paracasei subsp. paracasei IM1339


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: food additive Lactoseven

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Illumina MiSeq v3

text: Lacticaseibacillus paracasei subsp. paracasei IM1384

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: food additive BactoFlor fur Kinder

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lacticaseibacillus rhamnosus

characteristic: project name

text: Lacticaseibacillus rhamnosus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lacticaseibacillus rhamnosus IM561


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Bio-Kult infantis

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lacticaseibacillus rhamnosus

characteristic: organism

text: Lacticaseibacillus rhamnosus

text: Illumina MiSeq v3

text: Lacticaseibacillus rhamnosus IM1338


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Lacticaseibacillus rhamnosus

text: Lacticaseibacillus rhamnosus

text: Illumina MiSeq v3

text: Lacticaseibacillus rhamnosus IM1389

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: food additive EnteroDophilus

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lacticaseibacillus rhamnosus

characteristic: project name

text: Lacticaseibacillus rhamnosus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lacticaseibacillus rhamnosus IM1459


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Waya AB

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lactiplantibacillus plantarum

characteristic: organism

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

text: Lactiplantibacillus plantarum IM562


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: food additive Vivomixx

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Lactiplantibacillus plantarum

text: Lactiplantibacillus plantarum

text: Illumina MiSeq v3

text: Lactiplantibacillus plantarum IM1393

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: feed additive Jamieson Probiotic 30 Billion

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lactobacillus gasseri

characteristic: project name

text: Lactobacillus gasseri

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactobacillus gasseri IM1390


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: Linex

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Lactobacillus paragasseri

characteristic: organism

text: Lactobacillus paragasseri

text: Illumina MiSeq v3

text: Lactobacillus paragasseri IM216


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: food additive OMNi BiOTiC PANDA

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Lactococcus lactis subsp. lactis

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

text: Lactococcus lactis subsp. lactis IM1341

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: probiotic strain

text: food

text: food additive

text: food additive Treflor Gocce

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Limosilactobacillus reuteri

characteristic: project name

text: Limosilactobacillus reuteri

text: Illumina MiSeq v3

characteristic: sequencing method

text: Limosilactobacillus reuteri IM566


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: probiotic strain

characteristic: description

text: food

text: food additive

text: food additive Floractin

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Pediococcus pentosaceus

characteristic: organism

text: Pediococcus pentosaceus

text: Illumina MiSeq v3

text: Pediococcus pentosaceus IM811


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: probiotic strain

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: food additive Bio-Kult infantis

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Streptococcus thermophilus

text: Streptococcus thermophilus

text: Illumina MiSeq v3

text: Streptococcus thermophilus IM1340

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: protective culture

text: food

text: protective culture

text: meat protective culture Sacco Lyocarni BMX-37

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Latilactobacillus sakei

characteristic: project name

text: Latilactobacillus sakei

text: Illumina MiSeq v3

characteristic: sequencing method

text: Latilactobacillus sakei IM1465


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture Ryazhenka

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Enterococcus durans

characteristic: organism

text: Enterococcus durans

text: Illumina MiSeq v3

text: Enterococcus durans IM1426


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: starter culture

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: sturter culture Hela Germet

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Enterococcus hirae

text: Enterococcus hirae

text: Illumina MiSeq v3

text: Enterococcus hirae IM1454

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: starter culture

text: food

text: food additive

text: sturter culture BOLGARI

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lacticaseibacillus rhamnosus

characteristic: project name

text: Lacticaseibacillus rhamnosus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lacticaseibacillus rhamnosus IM1429


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture BOLGARI

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

characteristic: organism

text: Illumina MiSeq v3

text: Lactobacillus delbrueckii subsp. bulgaricus IM1430


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: starter culture

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: sturter culture Gedroogde Viili starter

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Lactococcus cremoris

text: Lactococcus cremoris

text: Illumina MiSeq v3

text: Lactococcus lactis subsp. cremoris IM1456

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: starter culture

text: food

text: food additive

text: sturter culture Biostart RP 100

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Lactococcus lactis subsp. lactis

characteristic: project name

text: Lactococcus lactis subsp. lactis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Lactococcus lactis subsp. lactis IM1409


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture Sacco Lyoflora B-7

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

characteristic: organism

text: Illumina MiSeq v3

text: Leuconostoc mesenteroides subsp. mesenteroides IM1476


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: starter culture

text: dairy product

characteristic: environment (biome)

text: cheese or cheese product

characteristic: environment (feature)

text: fresh curd cheese

characteristic: environment (material)

text: Slovenia

text: not provided

text: not provided

text: Leuconostoc pseudomesenteroides

text: Resistomes of probiotic and starter cultures as potential risk factors for the spread of antibiotic resistance

text: Leuconostoc pseudomesenteroides

text: Illumina MiSeq v3

text: Leuconostoc pseudomesenteroides IM1374

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: starter culture

text: food

text: food additive

text: sturter culture Diostart

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Levilactobacillus brevis

characteristic: project name

text: Levilactobacillus brevis

text: Illumina MiSeq v3

characteristic: sequencing method

text: Levilactobacillus brevis IM1457


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture Sacco MBP

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Levilactobacillus brevis

characteristic: organism

text: Levilactobacillus brevis

text: Illumina MiSeq v3

text: Levilactobacillus brevis IM1470


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: starter culture

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: sturter culture Sacco Lyoflora B-7

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Pediococcus acidilactici

text: Pediococcus acidilactici

text: Illumina MiSeq v3

text: Pediococcus acidilactici IM1475

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: starter culture

text: food

text: food additive

text: sturter culture Sacco Lyoflora B-7

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Pediococcus pentosaceus

characteristic: project name

text: Pediococcus pentosaceus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Pediococcus pentosaceus IM1473


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture Nitrostart G

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Staphylococcus carnosus

characteristic: organism

text: Staphylococcus carnosus

text: Illumina MiSeq v3

text: Staphylococcus carnosus IM1421


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: not provided

characteristic: collection date

text: starter culture

text: food

characteristic: environment (biome)

text: food additive

characteristic: environment (feature)

text: sturter culture Biostart RP 100

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: Staphylococcus xylosus

text: Staphylococcus xylosus

text: Illumina MiSeq v3

text: Staphylococcus xylosus IM1419

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: not provided

text: starter culture

text: food

text: food additive

text: sturter culture Hobbythek Quarkkultur

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

characteristic: investigation type

text: Streptococcus thermophilus

characteristic: project name

text: Streptococcus thermophilus

text: Illumina MiSeq v3

characteristic: sequencing method

text: Streptococcus thermophilus IM1424


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

text: starter culture

characteristic: description

text: food

text: food additive

text: sturter culture Kefirferment

text: not provided

text: not provided

text: not provided

characteristic: miscellaneous environmental package

text: Leuconostoc pseudomesenteroides

characteristic: organism

text: Leuconostoc pseudomesenteroides

text: Illumina MiSeq v3

text: Leuconostoc pseudomesenteroides IM1427


characteristic: ENA-CHECKLIST

text: Uppsala University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Uppsala University

text: eastern lowland gorilla

characteristic: common name

text: Gorilla dental calculus sample from museum specimen

text: Gorilla beringei graueri

text: Gorilla beringei graueri

text: Gorilla beringei graueri dental calculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Uppsala University

text: public

text: western lowland gorilla

text: Gorilla gorilla gorilla

text: Gorilla gorilla gorilla

text: Gorilla gorilla gorilla dental calculus


text: Uppsala University

text: public

text: eastern mountain gorilla

text: Gorilla beringei beringei

text: Gorilla beringei beringei

text: Gorilla beringei beringei dental calculus


text: public

tag: Namespace:Washington University School of Medicine

text: human

text: Homo sapiens

text: Homo sapiens


text: Washington University School of Medicine

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:Korea Advanced Institute of Science and Technology

text: sgRNA reads of plasmids, initial, glucose, CO2-H2, and Syngas

text: Eubacterium limosum

text: Eubacterium limosum

text: sgRNA reads


text: TEAGASC FOOD RESEARCH CENTRE

text: public

tag: Namespace:TEAGASC FOOD RESEARCH CENTRE

characteristic: collection date

text: gut recovered bacteria

text: gut

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: faecal sample ERC000015

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

characteristic: investigation type

text: Enterococcaceae bacterium

text: Mining the gut microbiome of elite athletes for novel probiotics

characteristic: project name

text: Enterococcaceae bacterium

text: Illumina whole genome sequencing

text: potential bacteriocin producing gut isolates


characteristic: External Id

text: IP

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: isolated from nasal swab

characteristic: clinical information

text: human

text: Protocols: Nasal swab from patients with symptoms of SARS-CoV-2. RNA extraction and qRT-PCR were carried out by the French National Center for Respiratory infection virus (32156327). Double-stranded cDNA was synthetized using random hexamers and the ProtoScript II first strand cDNA synthesis kit followed by the NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module from New England Biolabs. Indexed library preparation was made using the Nextera Flex for enrichment (Illumina) kit following the manufacturer’s protocol without modification. Indexed libraries were pooled according to the results of the RT-qPCR CT (cycle threshold) for SARS-CoV-2 of each sample. For Arbor Biosciences hybridization, a double capture was made according to the probes manufacturer’s protocol

characteristic: description

text: Severe acute respiratory syndrome coronavirus 2

characteristic: infect

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: nasal cavity

characteristic: organism part

text: Arbor Bioscience double capture hybridisation

characteristic: protocol

text: Homo sapiens

characteristic: viral load


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: IP

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: isolated from nasal swab

text: human

characteristic: common name

text: Protocols: Nasal swab from patients with symptoms of SARS-CoV-2 RNA extraction and qRT-PCR were carried out by the French National Center for Respiratory infection virus (32156327). double-stranded cDNA was synthetized using random hexamers and the ProtoScript II first strand cDNA synthesis kit followed by the NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module from New England Biolabs. Indexed library preparation was made using the Nextera Flex for enrichment (Illumina) kit following the manufacturer’s protocol without modification. Indexed libraries were pooled according to the results of the RT-qPCR CT (cycle threshold) for SARS-CoV-2 of each sample. For the Twist hybridization reactions, a modified Nextera Flex enrichment protocol was used.

text: Homo sapiens

text: Homo sapiens

text: nasal cavity

text: Twist Bioscience SARS-Cov-2 hybridisation

text: Homo sapiens

characteristic: title


characteristic: External Id

text: IP

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: isolated from nasal swab

text: human

text: Protocols: Nasal swab from patients with symptoms of SARS-CoV-2 RNA extraction and qRT-PCR were carried out by the French National Center for Respiratory infection virus (32156327). double-stranded cDNA was synthetized using random hexamers and the ProtoScript II first strand cDNA synthesis kit followed by the NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module from New England Biolabs. Indexed library preparation was made using the Nextera Flex for enrichment (Illumina) kit following the manufacturer’s protocol without modification. Indexed libraries were pooled according to the results of the RT-qPCR CT for SARS-CoV-2 of each sample. For Arbor Biosciences single hybridization, a modified Nextera Flex enrichment protocol was used.

text: Homo sapiens

text: Homo sapiens

text: nasal cavity

text: Homo sapiens


text: IP

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: isolated from nasal swab

characteristic: clinical information

text: human

text: Protocols: Nasal swab from patients with symptoms of SARS-CoV-2 RNA extraction and qRT-PCR were carried out by the French National Center for Respiratory infection virus (32156327). double-stranded cDNA was synthetized using random hexamers and the ProtoScript II first strand cDNA synthesis kit followed by the NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module from New England Biolabs. Indexed library preparation was made using the Nextera Flex for enrichment (Illumina) kit following the manufacturer’s protocol without modification.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: nasal cavity

text: Illumina Nextera Flex enrichment - metagenomics

text: Homo sapiens


text: IP

text: public

text: ArrayExpress

text: isolated from nasal swab

text: human

text: Protocols: Nasal swab from patients with symptoms of SARS-CoV-2 RNA extraction and qRT-PCR were carried out by the French National Center for Respiratory infection virus (32156327). Double-stranded cDNA was synthetized using random hexamers and the ProtoScript II first strand cDNA synthesis kit followed by the NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module from New England Biolabs. Indexed library preparation was made using the Nextera Flex for enrichment (Illumina) kit following the manufacturer’s protocol without modification. Indexed libraries were pooled according to the results of the RT-qPCR CT for SARS-CoV-2 of each sample. For the Twist hybridization reactions, a modified Nextera Flex enrichment protocol was used.

characteristic: infect

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: nasal cavity

characteristic: organism part

text: Twist Bioscience panviral hybridisation

characteristic: protocol

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF EDINBURGH

text: public

tag: Namespace:UNIVERSITY OF EDINBURGH

text: Sample 1 kept in clean seawater during the whole duration of the experiment.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Sample 2 kept in clean seawater during the whole duration of the experiment.

text: Halichondria panicea

text: Halichondria panicea


characteristic: External Id

text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 3 kept in clean seawater during the whole duration of the experiment.

text: Halichondria panicea

text: Halichondria panicea

characteristic: title


text: UNIVERSITY OF EDINBURGH

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Sample 2 kept in clean seawater with marine snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Sample 3 kept in clean seawater with marine snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 1 kept in clean seawater with marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 2 kept in clean seawater with marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 3 kept in clean seawater with marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 1 exposed to chemically enhanced water accommodated oil fraction during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 2 exposed to chemically enhanced water accommodated oil fraction during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 3 exposed to chemically enhanced water accommodated oil fraction during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 1 exposed to chemically enhanced water accommodated oil fraction with added marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 2 exposed to chemically enhanced water accommodated oil fraction with added marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


text: UNIVERSITY OF EDINBURGH

text: public

text: Sample 3 exposed to chemically enhanced water accommodated oil fraction with added marine oil snow during the exposure.

text: Halichondria panicea

text: Halichondria panicea


E-MTAB-11294:Sample 1

text: public

text: E-MTAB-11294:Sample 1

tag: Namespace:Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: immune cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: C56BL/6 mice (10 to 12-week-old) were immunized subcutaneously at the base of the tail with 100 μg of MOG (35-55) emulsified in complete Freund's adjuvant containing 500 μg of Mycobacterium tuberculosis. Pertussis toxin (200 ng; List Biological Laboratories) was injected intravenously at days 0 and 2 post-immunization. At day 17 post immunization, central nervous system CD45-positive immune cells were isolated and loaded onto a single channel of a 10x Chromium chip for each sample. The scRNA-seq libraries were generated using Chromium Next GEM Single Cell V(D)J Reagent Kit v.1.1 with Feature Barcoding (10X Genomics) according to the manufacturer’s protocol. Gene expression (mRNA) libraries were constructed. Briefly, cells were counted and up to 20 000 cells were loaded in the 10X Genomics Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq S2 flowcell (Illumina) with 26 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2, targeting a median depth of 50000 reads per cell for gene expression.

text: adult

characteristic: developmental stage

text: autoimmune encephalomyelitis

characteristic: disease

text: CD45 positive

characteristic: immunophenotype

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-11294:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France

characteristic: INSDC first public

text: public

text: E-MTAB-11294:Sample 2

text: ArrayExpress

text: immune cell

text: house mouse

characteristic: description

text: adult

text: autoimmune encephalomyelitis

text: CD45 positive

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

characteristic: organism part

text: Mus musculus

text: female

text: Sample 2


E-MTAB-11294:Sample 3

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11294:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: immune cell

text: house mouse

text: adult

text: autoimmune encephalomyelitis

text: CD45 positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: Sample 3

characteristic: title


E-MTAB-11294:Sample 4

text: public

text: E-MTAB-11294:Sample 4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: immune cell

characteristic: cell type

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

text: autoimmune encephalomyelitis

characteristic: disease

text: CD45 positive

characteristic: immunophenotype

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: Sample 4


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

tag: Namespace:Division of Computational Biology, University of Dundee

text: ArrayExpress

text: Protocols: in vitro cultures Quiagen RNA extraction Illumina PCR

characteristic: description

text: trypomastigote

text: Trypanosoma brucei TREU927

text: Trypanosoma brucei brucei TREU927

text: whole organism

text: Trypanosoma brucei brucei TREU927


characteristic: External Id

text: Division of Computational Biology, University of Dundee

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: trypomastigote

text: Trypanosoma brucei TREU927

characteristic: organism

text: Trypanosoma brucei brucei TREU927

text: whole organism

characteristic: organism part

text: Trypanosoma brucei brucei TREU927


text: University of Bayreuth

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Bayreuth

characteristic: Submitter Id

characteristic: collection date

text: Headwater stream

characteristic: environment (biome)

text: Headwater stream

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: MIMARKS-survey

characteristic: investigation type

text: unidentified bacterium

text: CAMPOS

characteristic: project name

text: unidentified bacterium

text: streambed sediment

characteristic: sediment environmental package

text: PacBio Sequel

characteristic: sequencing method

text: Streambed bacterial community

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bayreuth

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Downstream

characteristic: description

text: Headwater stream

text: Headwater stream

text: Sediment

text: Germany

text: MIMARKS-survey

text: unidentified bacterium

characteristic: organism

text: CAMPOS

text: unidentified bacterium

text: streambed sediment

text: PacBio Sequel

text: Streambed bacterial community


text: University of Bayreuth

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Confluence

text: Headwater stream

characteristic: environment (biome)

text: Headwater stream

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: MIMARKS-survey

text: unidentified bacterium

text: CAMPOS

text: unidentified bacterium

text: streambed sediment

text: PacBio Sequel

text: Streambed bacterial community


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR DE PARIS

text: public

tag: Namespace:INSTITUT PASTEUR DE PARIS

text: TechnoSuruga Laboratory Co. Ltd,Shimizu,Shizuoka,Japan

characteristic: collected by

text: Bacterial culture

text: Japan

characteristic: isolate

text: plaster wall surface of 1300-year-old mural paintings

characteristic: isolation source

text: Biological Resource Center of�Institut Pasteur, Paris, France

characteristic: lab host

text: Bordetella muralis

text: Bordetella muralis

text: Bordetella muralis strain

characteristic: title


text: INSTITUT PASTEUR DE PARIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Bacterial culture

characteristic: description

text: Japan

text: Bordetella tumbae

characteristic: organism

text: Bordetella tumbae

text: Bordetella tumbae strain


characteristic: ENA-CHECKLIST

text: INSTITUT PASTEUR DE PARIS

text: public

text: Bacterial culture

text: Japan

characteristic: geographic location (country and/or sea)

text: Bordetella tumulicola

text: Bordetella tumulicola

text: Bordetella tumulicola strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR DE PARIS

text: public

characteristic: collection date

text: nasopharynx

text: France

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Institut Pasteur, National Reference Center for Whooping Cough and Other�Bordetella�Infections, Paris, France.

characteristic: identified by

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica

text: Bacterial culture


characteristic: External Id

text: INSTITUT PASTEUR DE PARIS

text: public

text: France

text: diseased

text: Canis lupus

characteristic: isolate

characteristic: isolation source

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica

text: Bacterial culture

characteristic: title


text: INSTITUT PASTEUR DE PARIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: France

text: diseased

text: Sus domesticus

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica

text: Bacterial culture


text: FAU Erlangen

text: public

characteristic: SRA accession

tag: Namespace:FAU Erlangen

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Anti-HA ChIP of constitutively expressed HA_Meis1 in hematopoieitic cells coexpresssing HoxA9 and Pbx3

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of HA_Meis1_FKBP without dTAG (0h) in hematopoieitic cells coexpresssing HoxA9 and Pbx3

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of HA_Meis1_FKBP with dTAG (8h) in hematopoieitic cells coexpresssing HoxA9 and Pbx3

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-IgG (unspecific) ChIP of hematopoietic cells coexpressing HA-Meis1, HoxA9, and Pbx3

text: Mus musculus

text: Mus musculus

text: input


text: FAU Erlangen

text: public

text: house mouse

text: Anti-H3K27ac3 ChIP of hematopoietic cells coexpressing HA-Meis1, HoxA9, and Pbx3

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-H3K4me ChIP of hematopoietic cells coexpressing HA-Meis1, HoxA9, and Pbx3

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of constitutively expressed HA_HoxA9 in hematopoieitic cells coexpresssing Meis1 and Pbx3

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of constitutively expressed HA_Pbx3 in hematopoieitic cells coexpresssing Meis1 and HoxA9

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of constitutively expressed HA_Meis1 in hematopoieitic cells coexpresssing HoxA9FKBP without dTAG13 (0h not degraded)

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: Anti-HA ChIP of constitutively expressed HA_Meis1 in hematopoieitic cells coexpresssing HoxA9FKBP with dTAG13 (2h degraded)

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: nascent RNA seq of hematopoietic cells expressing HoxA9 and doxycycline inducible Meis1, non-induced 0h

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: nascent RNA seq of hematopoietic cells expressing HoxA9 and doxycycline inducible Meis1, induced for 72h

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: nascent RNA seq of hematopoietic cells expressing HoxA9 and degradable Meis1FKBP, not-degraded without dTAG (0h)

text: Mus musculus

text: Mus musculus


text: FAU Erlangen

text: public

text: house mouse

text: nascent RNA seq of hematopoietic cells expressing HoxA9 and degradable Meis1FKBP, after addition of dTAG and degradation (24h)

text: Mus musculus

text: Mus musculus


text: UNIVERSITY OF WARWICK

text: public

tag: Namespace:UNIVERSITY OF WARWICK

text: ArrayExpress

characteristic: broker name

text: Protocols: The strain used in this study is the original clinical motile isolate of NCTC 11168 from the National Collection of Type Cultures. The strain was routinely cultured on Campylobacter blood-free selective agar supplemented with CCDA (containing Cefoperazone and Amphotericin B) (Oxoid). After 24 hours of incubation, a loop of NCTC 11168 culture was transferred onto and incubated overnight on agar plates containing cation-adjusted Mueller-Hinton 2 (MH2) (Sigma-Aldrich) 1.5% agar (BactoTMAgar). %(kindly donated by Professor Charles Penn from the University of Birmingham)The culture was incubated at 37 \textdegree{}C in a variable atmosphere incubator (VAIN) (Whitley VA500 workstation cabinet), with the following atmospheric content: 90 % N2 (v/v), 6 % CO2 (v/v), 4 % O2 (v/v)). 3.5 mL of cell culture was killed by adding 0.5 volumes of cold (4 oC) killing buffer (20 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 20 mM NaN3). Cell cultures were spun down at 5000-10000 x g for 3-5 minutes, then snap frozen in liquid nitrogen and stored at -80 oC until further use. Sample pellets were placed on ice before extraction. Workspace and pipettes were cleaned with RNaseZapTM (Sigma-Aldrich) prior to RNA extraction. Nuclease-free molecular biology grade water (Sigma-Aldrich), RNase-free filter tips, RNase-free eppendorf tubes (Sarstedt), and RNase-free 15 mL or 50 mL tubes (Falcon) were used throughout RNA extraction protocols. All centrifugation steps were carried out on Sigma 1-14K microcentrifuge (Sigma).The pellet was resuspended in 600 ul of LETS buffer (0.1M LiCl, 0.01M Na2EDTA, 0.01M Tris-Cl (pH 7.4), 0.2%SDS) and transferred to Lysing Matrix B, 0.1 mm tubes (MP biomedicalsTM). The tubes were placed in a FastPrep Homogenizer (MP biomedicalsTM) to perform 3 rounds of bead-beating at a speed of 6.0 m/s for 40 seconds, with a 5 minutes pause between rounds. The samples were then centrifugated at 13000 x g for 10 minutes at 4 oC. Afterwards, proteins and nucleic acids were separated from the cell debris by centrifuging at 13000 rpm at 4 oC for 10 minutes. RNA was phase-separated by 2 rounds of 125:24:1 Phenol/Chloroform/isoamylalcohol (PCI) and one round of 24:1 chloroform/isoamyl alcohol. The upper phase was mixed with 0.1 volume of 3M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 oC.After overnight precipitation, samples were centrifugated at top speed at 4 oC for 15 minutes. The supernatant was removed and pellets washed (without resuspending) with fresh 70% ethanol twice. Pellets were air-dried for 15 minutes before resuspending in 50 µL of RNase-free water. The resuspended RNA was incubated on ice for three hours, then 30 minutes at room temperature. RNA samples from all three biological replicates from each condition were diluted to around 100 ng/ul and pooled together for Cappable-seq processing detailed in Ettwiller et al. A control sample was used which omitted the Streptavidin capture step.The libraries were created from the Cappable-seq processed RNA pool using NEBNext Small RNA Library Prep Set for Illumina (NEB). Note that the control pool and the Cappable-seq enriched pool were PCR amplified for 12 and 18 cycles respectively.

text: wild type

characteristic: genotype

text: Exponential phase, TSS not enriched

characteristic: growth condition

text: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

text: Control


characteristic: External Id

text: UNIVERSITY OF WARWICK

text: public

text: ArrayExpress

text: wild type

text: Exponential phase, TSS enriched

text: Enriched


text: UNIVERSITY OF WARWICK

text: public

text: ArrayExpress

text: Protocols: The strain used in this study is the original clinical motile isolate of NCTC 11168 from the National Collection of Type Cultures. The strain was routinely cultured on Campylobacter blood-free selective agar supplemented with CCDA (containing Cefoperazone and Amphotericin B) (Oxoid). After 24 hours of incubation, a loop of NCTC 11168 culture was transferred onto and incubated overnight on agar plates containing cation-adjusted Mueller-Hinton 2 (MH2) (Sigma-Aldrich) 1.5% agar (BactoTMAgar). %(kindly donated by Professor Charles Penn from the University of Birmingham)The culture was incubated at 37 \textdegree{}C in a variable atmosphere incubator (VAIN) (Whitley VA500 workstation cabinet), with the following atmospheric content: 90 % N2 (v/v), 6 % CO2 (v/v), 4 % O2 (v/v)). 3.5 mL of cell culture was killed by adding 0.5 volumes of cold (4 oC) killing buffer (20 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 20 mM NaN3). Cell cultures were spun down at 5000-10000 x g for 3-5 minutes, then snap frozen in liquid nitrogen and stored at -80 oC until further use. Sample pellets were placed on ice before extraction. Workspace and pipettes were cleaned with RNaseZapTM (Sigma-Aldrich) prior to RNA extraction. Nuclease-free molecular biology grade water (Sigma-Aldrich), RNase-free filter tips, RNase-free eppendorf tubes (Sarstedt), and RNase-free 15 mL or 50 mL tubes (Falcon) were used throughout RNA extraction protocols. All centrifugation steps were carried out on Sigma 1-14K microcentrifuge (Sigma).The pellet was resuspended in 600 ul of LETS buffer (0.1M LiCl, 0.01M Na2EDTA, 0.01M Tris-Cl (pH 7.4), 0.2%SDS) and transferred to Lysing Matrix B, 0.1 mm tubes (MP biomedicalsTM). The tubes were placed in a FastPrep Homogenizer (MP biomedicalsTM) to perform 3 rounds of bead-beating at a speed of 6.0 m/s for 40 seconds, with a 5 minutes pause between rounds. The samples were then centrifugated at 13000 x g for 10 minutes at 4 oC. Afterwards, proteins and nucleic acids were separated from the cell debris by centrifuging at 13000 rpm at 4 oC for 10 minutes. RNA was phase-separated by 2 rounds of 125:24:1 Phenol/Chloroform/isoamylalcohol (PCI) and one round of 24:1 chloroform/isoamyl alcohol. The upper phase was mixed with 0.1 volume of 3M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 oC.After overnight precipitation, samples were centrifugated at top speed at 4 oC for 15 minutes. The supernatant was removed and pellets washed (without resuspending) with fresh 70% ethanol twice. Pellets were air-dried for 15 minutes before resuspending in 50 µL of RNase-free water. The resuspended RNA was incubated on ice for three hours, then 30 minutes at room temperature. This protocol was adapted from Shishkin et al. 2015.

text: wild type

characteristic: title


text: UNIVERSITY OF WARWICK

characteristic: INSDC center name

text: public

text: ArrayExpress

text: wild type

text: acid


text: UNIVERSITY OF WARWICK

characteristic: INSDC first public

text: public

text: ArrayExpress

text: wild type

text: ana


text: UNIVERSITY OF WARWICK

characteristic: INSDC last update

text: public

text: ArrayExpress

text: wild type

text: cold


text: UNIVERSITY OF WARWICK

text: public

characteristic: INSDC status

text: ArrayExpress

text: wild type

text: heat


text: UNIVERSITY OF WARWICK

text: public

characteristic: SRA accession

text: ArrayExpress

text: wild type

text: nacl


text: UNIVERSITY OF WARWICK

text: public

characteristic: Submitter Id

text: ArrayExpress

text: wild type

text: oxidative


text: UNIVERSITY OF WARWICK

text: public

text: ArrayExpress

text: wild type

text: starv


text: UNIVERSITY OF WARWICK

text: public

text: ArrayExpress

text: wild type

text: GSNO


text: WAGENINGEN UNIVERSITY

text: public

tag: Namespace:WAGENINGEN UNIVERSITY

text: 3 weeks

characteristic: age

text: Brussels sprouts

characteristic: common name

text: Cyrus

characteristic: cultivar

text: Primary root harvested at 0, 3, 6, 9, 24, 48 hours after Delia radicum infestation, with or without leaf herbivores present

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: C01 : Control


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: C02 : Control


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C03 : Control

characteristic: title


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C04 : Control


text: WAGENINGEN UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B01 : Brevicoryne brassicae


text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

characteristic: age

text: Brussels sprouts

characteristic: common name

text: Cyrus

characteristic: cultivar

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B02 : Brevicoryne brassicae


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: B03 : Brevicoryne brassicae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B04 : Brevicoryne brassicae


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: P01 : Plutella xylostella


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: P02 : Plutella xylostella

characteristic: title


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: P03 : Plutella xylostella


text: WAGENINGEN UNIVERSITY

text: public

characteristic: Submitter Id

text: 3 weeks

characteristic: age

text: Brussels sprouts

characteristic: common name

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: P04 : Plutella xylostella


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: cultivar

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

text: Brassica oleracea var. gemmifera

text: C07 : Control


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: C08 : Control


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C09 : Control


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: C10 : Control


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B07 : Brevicoryne brassicae

characteristic: title


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

characteristic: age

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B08 : Brevicoryne brassicae


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

characteristic: common name

text: Cyrus

characteristic: cultivar

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B09 : Brevicoryne brassicae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

text: Brassica oleracea var. gemmifera

text: B10 : Brevicoryne brassicae


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: P07 : Plutella xylostella


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: P08 : Plutella xylostella


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: P09 : Plutella xylostella


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: P10 : Plutella xylostella

characteristic: title


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

characteristic: age

text: Brussels sprouts

characteristic: common name

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: D07 : Delia radicum


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: cultivar

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: D08 : Delia radicum


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

text: Brassica oleracea var. gemmifera

text: D09 : Delia radicum


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: D10 : Delia radicum


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: BD07 : Brevicoryne + Delia


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: BD08 : Brevicoryne + Delia


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

characteristic: age

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: BD09 : Brevicoryne + Delia

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

characteristic: common name

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: BD10 : Brevicoryne + Delia


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: cultivar

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: PD07 : Plutella + Delia


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

text: Brassica oleracea var. gemmifera

text: PD08 : Plutella + Delia


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: PD09 : Plutella + Delia


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: PD10 : Plutella + Delia


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

characteristic: age

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: C13 : Control


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C14 : Control

characteristic: title


characteristic: External Id

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

characteristic: common name

text: Cyrus

characteristic: cultivar

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C15 : Control


text: WAGENINGEN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

characteristic: description

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: C16 : Control


text: WAGENINGEN UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: organism part

text: Brassica oleracea var. gemmifera

text: B13 : Brevicoryne brassicae


text: WAGENINGEN UNIVERSITY

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

text: Primary root

characteristic: sampling time point

text: Brassica oleracea var. gemmifera

text: B14 : Brevicoryne brassicae


characteristic: ENA-CHECKLIST

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

characteristic: age

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

characteristic: genotype

text: Brassica oleracea var. gemmifera

text: Primary root

text: Brassica oleracea var. gemmifera

text: B15 : Brevicoryne brassicae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: WAGENINGEN UNIVERSITY

text: public

text: 3 weeks

text: Brussels sprouts

text: Cyrus

text: Brassica oleracea var. gemmifera

text: Brassica oleracea var. gemmifera

characteristic: organism

text: Primary root

text: Brassica oleracea var. gemmifera

text: B16 : Brevicoryne brassicae