text: Thuenen Institute of Wood Research

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text: Quercus

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text: wood decay metagenome


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Thuenen Institute of Wood Research

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

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tag: Namespace:Thuenen Institute of Wood Research

characteristic: Submitter Id

characteristic: collection date

text: Trashcan

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: Abies alba

characteristic: host scientific name

text: wood

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characteristic: organism

text: wood decay metagenome

characteristic: title


text: Thuenen Institute of Wood Research

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text: Robinia pseudoacacia

text: wood

text: 53.50056213265332, 10.19179938440266

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text: Thuenen Institute of Wood Research

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text: Picea abies

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text: 53.469734899757846, 9.940208718903785

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: Larix

text: wood

text: 53.469734899757846, 9.940208718903785

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: Robinia pseudoacacia

text: wood

text: 53.45864497692408, 9.979791681619798

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: Robinia pseudoacacia

text: wood

text: 53.45864497692408, 9.979791681619798

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: Lophira alata

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text: Pseudotsuga menziesii

text: wood

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text: Pseudotsuga menziesii

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text: Pinus sylvestris

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text: Pinus sylvestris

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text: Pseudotsuga menziesii

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text: Quercus

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text: Robinia pseudoacacia

text: wood

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text: Robinia pseudoacacia

text: wood

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text: public

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text: Quercus

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text: wood decay metagenome

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text: 53.50056213265332, 10.19179938440266

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text: 53.50056213265332, 10.19179938440266

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: Robinia pseudoacacia

text: wood

text: 53.50056213265332, 10.19179938440266

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

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text: 53.469734899757846, 9.940208718903785

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text: Thuenen Institute of Wood Research

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text: Larix

text: wood

text: 53.469734899757846, 9.940208718903785

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

text: public

text: Playground

text: Germany

text: Robinia pseudoacacia

text: wood

text: 53.45864497692408, 9.979791681619798

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

text: public

text: Shelter

text: Germany

text: Robinia pseudoacacia

text: wood

text: 53.45864497692408, 9.979791681619798

text: wood decay metagenome

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text: Thuenen Institute of Wood Research

text: public

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text: Germany

text: Lophira alata

text: wood

text: 53.45613501054012, 9.97447052905659

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Bridge

text: Germany

text: Pseudotsuga menziesii

text: wood

text: 53.45613501054012, 9.97447052905659

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

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text: Germany

text: Quercus

text: wood

text: 53.45508863081172, 9.970022007867595

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Parkbench

text: Germany

text: Pseudotsuga menziesii

text: wood

text: 53.5690729264789, 10.052682185887182

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Fencepost

text: Germany

text: Quercus

text: wood

text: 53.68566608304693, 10.084113445207267

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Fence

text: Germany

text: Pinus sylvestris

text: wood

text: 53.68466678010054, 10.085227184720603

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Parkbench

text: Germany

text: Quercus

text: wood

text: 53.50139373047282, 10.019625921752118

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Playground

text: Germany

text: Quercus

text: wood

text: 53.50139373047282, 10.019625921752118

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Parkbench

text: Germany

text: Pinus sylvestris

text: wood

text: 53.49823603282457, 10.015065140236837

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Parkbench

text: Germany

text: Pseudotsuga menziesii

text: wood

text: 53.49823603282457, 10.015065140236837

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Parkbench

text: Germany

text: Pinus sylvestris

text: wood

text: 53.517917917921224, 9.990152149155902

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Playground

text: Germany

text: Quercus

text: wood

text: 53.55524472754944, 9.958927872208651

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Playground

text: Germany

text: Robinia pseudoacacia

text: wood

text: 53.458449217106605, 9.93388967432207

text: wood decay metagenome

text: wood decay metagenome


text: Thuenen Institute of Wood Research

text: public

text: Playground

text: Germany

text: Quercus

text: wood

text: 53.487848283785084, 10.14838901414573

text: wood decay metagenome

text: wood decay metagenome


text: Centro Nacional de Análisis Genómico

characteristic: GAL

text: Not collected

text: EarlhamInstitute

text: public

text: COPO

characteristic: broker name

text: MARC VENTURA

text: CENTER FOR ADVANCED STUDIES OF BLANES (CEAB-CSIC)

characteristic: collecting institution

characteristic: collector ORCID ID

unit: m

characteristic: elevation

text: Spain

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: CATALONIA|EBRO DELTA, ICHTYOLOGICAL INSTITUTE

characteristic: geographic location (region and locality)

text: CULTURE

characteristic: habitat

text: Nati Franch

text: Delta de l'Ebre Natural Park

text: adult

characteristic: lifestage

text: Valencia hispanica

text: MUSCLE

characteristic: organism part

text: SPAIN/CATALONIA/LLACUNES DE SANTES CREUS

characteristic: original collection location

characteristic: original geographic location (latitude)

characteristic: original geographic location (longitude)

text: ERGA

characteristic: project name

text: NOT PROVIDED

characteristic: proxy voucher

text: caught with fyke net

characteristic: sample collection device or method

text: Javier Palma Guerrero | Rosa Fernandez

characteristic: sample coordinator

characteristic: sample coordinator ORCID ID

text: INSTITUTE OF EVOLUTIONARY BIOLOGY | INSTITUTE OF EVOLUTIONARY BIOLOGY

characteristic: sample coordinator affiliation

characteristic: sample derived from

text: Valencia hispanica

text: FEMALE

characteristic: sex

text: ERGA MV 414X 001

text: MNCN ICTIO 296.954

text: 6e590940-e7bc-4a4f-a1dc-837f01c5c491-erga

characteristic: tolid


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Senckenber Biodiversity and Climate Research Centre Frankfurt

characteristic: Submitter Id

characteristic: collection date

text: specimen

characteristic: description

text: Italy

characteristic: geographic location (country and/or sea)

text: Luis J. Chueca

text: Candidula cavannae

characteristic: organism

text: Candidula cavannae

characteristic: title


text: Senckenber Biodiversity and Climate Research Centre Frankfurt

text: public

text: specimen

text: Italy

text: Luis J. Chueca

text: Candidula cavannae

text: Candidula cavannae


text: public

text: specimen

text: Italy

text: Luis J. Chueca

text: Candidula conglomeratica

text: Candidula conglomeratica


text: public

text: specimen

text: Italy

text: Luis J. Chueca

text: Candidula unifasciata

text: Candidula unifasciata


text: public

text: specimen

text: Italy

text: Luis J. Chueca

text: Xerogyra spadae

text: Xerogyra spadae


text: public

text: specimen

text: Spain

text: Luis J. Chueca

text: Trochoidea elegans

text: Trochoidea elegans


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

tag: Namespace:PhD fellow, Norwegian University of Life science

text: ArrayExpress

characteristic: broker name

text: not collected

text: Atlantic salmon

characteristic: common name

text: Protocols: RNA seq analysis was conducted on IFNα_ISAV/ IFNα_IPNV (n=4) treatment groups at 2 hours post-infection and results were compared with wild SHK-1 cells (n=4). For Knock out (KO) experiment, IFNα_ISAV/ IFNα_IPNV (n=4) treatment groups at 2 hours post-infection were used as control and below KO groups were used as treatment groups. The number of each group was mentioned in brackets. KO_CRFB1a_IFNα_ISAV_SHK-1 (n=3) KO_CRFB5a_IFNα_ISAV_SHK_1 (n=3) KO_I10R2_IFNα_ISAV_SHK-1 (n=2) KO_I10Rb_IFNα_ISAV_SHK-1 (n=3) KO_IFNGR2b_IFNα_ISAV_SHK-1 (n=3) KO_CRFB1a_IFNα_IPNV_SHK-1 (n=3) KO_CRFB5a_IFNα_IPNV_SHK_1 (n=3) KO_I10R2_IFNα_IPNV_SHK-1 (n=2) KO_IFNGR2b_IFNα_IPNV_SHK-1 (n=3) KO_I10Rb_IFNα_IPNV_SHK-1 (n=3) KO_All_IFNα_ISAV_SHK-1 (n=2) KO_All_IFNα_IPNV_SHK-1 (n=2) Total RNA was extracted from collected cells by using the Direct-zol RNA Microprep Kits (Zymo) using the manufacturer’s protocol. The RNA purity was measured using a Tape station, and the RNA concentration was determined using spectrophotometry (Nanodrop ND1000). Novogene mRNA-seq Services did library preparation. Briefly, the library is prepared according to Salmo salar, and subsequently tested for its quality (Library QC).

text: wild type genotype

characteristic: genotype

text: not collected

text: infectious pancreatic necrosis virus

characteristic: infect

text: not applicable

characteristic: isolate

text: Salmo salar

text: Salmo salar

text: head kidney

characteristic: organism part

text: Salmo salar

text: IFNα

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: External Id

text: PhD fellow, Norwegian University of Life science

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: not collected

text: Atlantic salmon

text: wild type genotype

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: Atlantic salmon

characteristic: description

text: CRFB1a, CRFB5a, I10R2, IFNGR2b, I10Rb and IFNGR2b knockout

text: not collected

characteristic: geographic location (country and/or sea)

text: infectious pancreatic necrosis virus

text: not applicable

text: Salmo salar

characteristic: organism

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: Atlantic salmon

characteristic: common name

characteristic: genotype

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: ArrayExpress

text: not collected

text: Atlantic salmon

text: CRFB1a knockout

text: not collected

text: infectious pancreatic necrosis virus

characteristic: infect

text: not applicable

characteristic: isolate

text: Salmo salar

text: Salmo salar

text: head kidney

characteristic: organism part

text: Salmo salar

text: IFNα

characteristic: stimulus


characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: Atlantic salmon

text: CRFB1a knockout

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: not collected

text: Atlantic salmon

characteristic: description

text: CRFB5a knockout

text: not collected

characteristic: geographic location (country and/or sea)

text: infectious pancreatic necrosis virus

text: not applicable

text: Salmo salar

characteristic: organism

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: Atlantic salmon

characteristic: common name

text: CRFB5a knockout

characteristic: genotype

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: not collected

text: Atlantic salmon

text: I10R2 knockout

text: not collected

text: infectious pancreatic necrosis virus

characteristic: infect

text: not applicable

characteristic: isolate

text: Salmo salar

text: Salmo salar

text: head kidney

characteristic: organism part

text: Salmo salar

text: IFNα

characteristic: stimulus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: Atlantic salmon

text: I10R2 knockout

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: ArrayExpress

text: not collected

text: Atlantic salmon

characteristic: description

text: IFNGR2b knockout

text: not collected

characteristic: geographic location (country and/or sea)

text: infectious pancreatic necrosis virus

text: not applicable

text: Salmo salar

characteristic: organism

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: Atlantic salmon

characteristic: common name

text: I10Rb knockout

characteristic: genotype

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: not collected

text: Atlantic salmon

text: I10Rb knockout

text: not collected

text: infectious pancreatic necrosis virus

characteristic: infect

text: not applicable

characteristic: isolate

text: Salmo salar

text: Salmo salar

text: head kidney

characteristic: organism part

text: Salmo salar

text: IFNα

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: Atlantic salmon

text: IFNGR2b knockout

text: not collected

text: infectious salmon anemia virus

text: not applicable

text: Salmo salar

text: Salmo salar

text: head kidney

text: Salmo salar

text: IFNα


E-MTAB-13068:Wild cells- SHK-1 cells

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13068:Wild cells- SHK-1 cells

text: ArrayExpress

text: not collected

text: Atlantic salmon

characteristic: description

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Salmo salar

characteristic: organism

text: Salmo salar

text: head kidney

text: Salmo salar

text: Wild cells- SHK-1 cells

characteristic: title


AP 52.1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Yeast Genomics Lab@Nova, UNL, Portugal

characteristic: INSDC last update

text: public

text: AP 52.1

tag: Namespace:Yeast Genomics Lab@Nova, UNL, Portugal

text: not provided

text: baker's yeast

characteristic: common name

text: Isolated from camel fermented milk (dough)

text: Iran

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Dairy


AP 53.1

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: AP 53.1

text: not provided

text: baker's yeast

text: Isolated from cow fermented milk (dough)

text: Iran

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Dairy


AP 54.1

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: AP 54.1

text: not provided

text: baker's yeast

text: Iran

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Dairy


text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: not provided

text: baker's yeast

text: Isolated from acidified milk 'nunu'

text: Ghana

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Dairy


text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: not provided

text: baker's yeast

text: Isolated from sorghum beer

text: Ghana

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: African Beer


TBRC 9268

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9268

text: not provided

text: baker's yeast

text: Isolated from Nypa palm fruit stem sap

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 9269

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9269

text: not provided

text: baker's yeast

text: Isolated from Nypa palm fruit stem sap

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 9270

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9270

text: not provided

text: baker's yeast

text: Isolated from Toddy palm inflorescence sap

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 9271

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9271

text: not provided

text: baker's yeast

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 9266

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9266

text: not provided

text: baker's yeast

text: Isolated from coconut inflorescence sap

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 9267

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 9267

text: not provided

text: baker's yeast

text: Isolated from coconut inflorescence sap

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Philippines


TBRC 618

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 618

text: not provided

text: baker's yeast

text: Isolated from moss

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 618


TBRC 3578

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3578

text: not provided

text: baker's yeast

text: Isolated from lichen

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 3578


TBRC 3589

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3589

text: not provided

text: baker's yeast

text: Isolated from insect frass

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 3589


TBRC 3587

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3587

text: not provided

text: baker's yeast

text: Isolated from insect frass

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai I


TBRC 617

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 617

text: not provided

text: baker's yeast

text: Isolated from moss

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai I


TBRC 3978

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3978

text: not provided

text: baker's yeast

text: Isolated from mushroom

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai I


TBRC 3977

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3977

text: not provided

text: baker's yeast

text: Isolated from mushroom

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai I


TBRC 616

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 616

text: not provided

text: baker's yeast

text: Isolated from insect frass

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai I


TBRC 3588

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3588

text: not provided

text: baker's yeast

text: Isolated from mushroom

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 3588


text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: not provided

text: baker's yeast

text: Isolated from wood in decomposition (Hybrid S.cer x S.par)

text: Brazil

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: WB1 - CHN V


text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: not provided

text: baker's yeast

text: Isolated from wood in decomposition

text: Brazil

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: WB1 - CHN V


TBRC 3580

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3580

text: not provided

text: baker's yeast

text: Isolated from lichen

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 3580


CBS 1419

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: CBS 1419

text: not provided

text: baker's yeast

text: Isolated from palm wine from Elaeis guineensis

text: Ghana

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: West Africa


TBRC 614

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 614

text: not provided

text: baker's yeast

text: Isolated from insect frass

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai II


TBRC 615

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 615

text: not provided

text: baker's yeast

text: Isolated from moss

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai II


TBRC 3581

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3581

text: not provided

text: baker's yeast

text: Isolated from tree exudate

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Thai II


TBRC 3614

text: Yeast Genomics Lab@Nova, UNL, Portugal

text: public

text: TBRC 3614

text: not provided

text: baker's yeast

text: Isolated from lichen

text: Thailand

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: TBRC 3614


Plesio

text: MNHN

text: public

text: Plesio

text: Plesiomonas shigelloides 7A

text: Plesiomonas shigelloides

text: Plesiomonas shigelloides

text: Plesiomonas shigelloides


E-MTAB-13095:Sample 11

text: public

text: E-MTAB-13095:Sample 11

tag: Namespace:Laboratory for Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: Protocols: AML cell lines were pre-treated with siRNA against S100A9 for 24 hours and were afterwards incubated with ABT-199 for an additional 24 hours. Total RNA was extracted and purified using the NucleoSpin RNA plus kit (Macherey–Nagel, Düren, Germany). Sample quality was checked by calculating the RNA integrity number (RIN value) using fragment analyser (Agilent), with 3 biological replicates from each group. The RNA sequencing (RNA-seq) library preparation was performed with 150 ng RNA using the Illumina KAPA RNA HyperPrep kit with RiboErase (HMR) (Illumina, Cambridge, UK).

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 11


E-MTAB-13095:Sample 3

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Laboratory for Hematology and Immunology, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 3


E-MTAB-13095:Sample 7

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 7

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 7


E-MTAB-13095:Sample 15

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 15

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 15

characteristic: title


E-MTAB-13095:Sample 19

text: public

text: E-MTAB-13095:Sample 19

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 19


E-MTAB-13095:Sample 23

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 23

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 23


E-MTAB-13095:Sample 12

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 12

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 12


E-MTAB-13095:Sample 4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 4

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 4


E-MTAB-13095:Sample 8

text: public

text: E-MTAB-13095:Sample 8

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 8

characteristic: title


E-MTAB-13095:Sample 16

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 16

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 16


E-MTAB-13095:Sample 20

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 20

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 20


E-MTAB-13095:Sample 24

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 24

text: ArrayExpress

text: not collected

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 24


E-MTAB-13095:Sample 1

text: public

text: E-MTAB-13095:Sample 1

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 1


E-MTAB-13095:Sample 5

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 5

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 5

characteristic: title


E-MTAB-13095:Sample 9

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 9


E-MTAB-13095:Sample 13

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 13

text: ArrayExpress

text: not collected

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 13


E-MTAB-13095:Sample 17

text: public

text: E-MTAB-13095:Sample 17

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 17


E-MTAB-13095:Sample 21

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 21

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 21


E-MTAB-13095:Sample 10

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 10

characteristic: title


E-MTAB-13095:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 2

text: ArrayExpress

text: not collected

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: Sample 2


E-MTAB-13095:Sample 6

text: public

text: E-MTAB-13095:Sample 6

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: Sample 6


E-MTAB-13095:Sample 14

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13095:Sample 14

text: ArrayExpress

text: not collected

text: human

text: adult

text: acute myeloid leukemia

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 14


E-MTAB-13095:Sample 18

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13095:Sample 18

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 18


E-MTAB-13095:Sample 22

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: E-MTAB-13095:Sample 22

text: ArrayExpress

text: not collected

text: human

characteristic: description

text: adult

text: acute myeloid leukemia

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 22

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: not provided

text: malaria parasite P. falciparum

characteristic: common name

text: not provided

text: Plasmodium falciparum

text: Plasmodium falciparum


characteristic: ENA-CHECKLIST

text: UOM

text: public

text: ArrayExpress

characteristic: broker name

text: natural killer cell

text: not collected

text: human

text: Protocols: Peripheral blood leukocyte cones from healthy human donors were acquired from the National blood service under ethics license REC 05/Q0401/108 (University of Manchester). Peripheral blood mononuclear cells (PBMCs) were purified by density gradient centrifugation using Ficoll-Paque (GE Healthcare; Life Sciences) and NK cells isolated by negative selection (NK cell isolation kit; Miltenyi Biotech). NK cells were cultured at 37⁰C and 5% CO₂ in Dulbecco’s Modified Eagle Medium (DMEM) medium (Sigma) containing 30% Ham’s F-12, 10% human serum (Sigma), 1% nonessential amino acids (Sigma), 1 mM sodium pyruvate (Sigma), 2 mM L-glutamine, 50 U/mL penicillin-streptomycin, and 50 μM 2-mercaptoethanol (Gibco) (NK cell clone medium). NK cells were also supplemented with 200 U/mL interleukin-2 (Roche) and rested for 6 days prior to experiments. To investigate the effects of PGE₂, NK cell cultures were additionally supplemented with 500 ng/mL synthetic PGE₂ (Sigma) 24 hours prior to cell harvesting and lysis. NK cells were cultured at 37⁰C and 5% CO₂ in Dulbecco’s Modified Eagle Medium (DMEM) medium (Sigma) containing 30% Ham’s F-12, 10% human serum (Sigma), 1% nonessential amino acids (Sigma), 1 mM sodium pyruvate (Sigma), 2 mM L-glutamine, 50 U/mL penicillin-streptomycin, and 50 μM 2-mercaptoethanol (Gibco) (NK cell clone medium). NK cells were also supplemented with 200 U/mL interleukin-2 (Roche) and rested for 6 days prior to experiments. After being rested for six days the NK cells were left untreated or supplemented with 500 ng/mL synthetic PGE₂ (Sigma) 24 hours prior to cell harvesting and lysis. NK cells were re-suspended in RLT buffer (RNeasy lysis buffer; Qiagen) containing 0.01% β-mercaptoethanol to lyse cells and stored at -80⁰C prior to RNA extraction. RNA was extracted from thawed samples using the RNeasy mini kit (Qiagen) as per the manufacturer’s instructions. mRNA libraries were prepared using the Illumina stranded mRNA prep kit.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Friedrich Schiller University Jena Institute of Biodiversity Aquatic Geomicrobiology Group

text: ArrayExpress

text: not collected

text: Protocols: Biomass was harvested from mid-exponential cultures by means of centrifugation. Pseudomonas alloputida KT2440 was grown using MP medium to mid-exponential phase, using phenylethanol (5 mM) as carbon and energy source. Cultures were grown with different lanthanide elements (La, Nd, Er, a lanthanide cocktail [Ce, Nd, Dy, Ho, Er, Yb]; 50 nM) or without lanthanide addition. Total RNA was extracted with TRI reagent (Applied Biosystems), and mRNA was enriched using the RiboMinus bacteria 2.0 transcriptome isolation kit (Invitrogen). Sequencing libraries were prepared with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs).

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: MP medium supplemented with 5 mM pheylethanol

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Pseudomonas putida

text: Pseudomonas putida

text: whole organism

characteristic: replicate

text: Pseudomonas putida

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Friedrich Schiller University Jena Institute of Biodiversity Aquatic Geomicrobiology Group

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

characteristic: description

text: wild type genotype

text: not collected

text: not applicable

text: Pseudomonas putida

characteristic: organism

text: Pseudomonas putida

text: whole organism

text: Pseudomonas putida

characteristic: title


SAMIN0003503-10619 Sample

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: SAMIN0003503-10619 Sample

tag: Namespace:Dr. Sarita Mohapatra, All Indian Institute of Medical Sciences

text: IBDC

characteristic: broker name

characteristic: common name

text: Emerging drug resistance in community-acquired urinary tract infection and molecular insights into dynamics of resistance traits in Indian isolates- A multi-centric cross-sectionalstudy

text: India

text: Delhi

characteristic: geographic location (region and locality)

text: Urinary tract infection

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: isolate

text: Urine

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: 10619 Sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Dr. Sarita Mohapatra, All Indian Institute of Medical Sciences

text: public

characteristic: SRA accession

text: IBDC

text: India

characteristic: geographic location (country and/or sea)

text: India-Delhi

text: Urinary tract infection

text: Homo sapiens

text: isolate

characteristic: isolate

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: IBDC

characteristic: collection date

characteristic: description

text: India

text: India-Bhubneshwar

text: Urinary tract infection

text: Homo sapiens

text: isolate

text: Urine

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: IBDC

text: India

text: India-Jodhpur

text: Urinary tract infection

text: Homo sapiens

text: isolate

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

characteristic: title


text: public

characteristic: INSDC status

text: IBDC

characteristic: broker name

characteristic: common name

text: India

text: India -Bangalore

characteristic: geographic location (region and locality)

text: Urinary tract infection

characteristic: host health state

text: Homo sapiens

text: isolate

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: IBDC

text: India

characteristic: geographic location (country and/or sea)

text: India-Bhubneshwar

text: Urinary tract infection

text: Homo sapiens

characteristic: host scientific name

text: isolate

text: Urine

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: IBDC

characteristic: collection date

text: India

text: India -Bangalore

text: Urinary tract infection

text: Homo sapiens

text: isolate

characteristic: isolate

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: IBDC

characteristic: description

text: India

text: India-Jodhpur

text: Urinary tract infection

text: Homo sapiens

text: isolate

text: Urine

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


text: public

characteristic: INSDC status

text: IBDC

characteristic: broker name

characteristic: common name

text: India

text: India-Delhi

characteristic: geographic location (region and locality)

text: Urinary tract infection

text: Homo sapiens

text: isolate

text: Escherichia coli

text: Escherichia coli

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: IBDC

text: India

characteristic: geographic location (country and/or sea)

text: India-Delhi

text: Urinary tract infection

characteristic: host health state

text: Homo sapiens

text: isolate

text: Urine

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: IBDC

characteristic: collection date

text: India

text: India -Bangalore

text: Urinary tract infection

text: Homo sapiens

characteristic: host scientific name

text: isolate

text: Urine

text: Escherichia coli

text: Escherichia coli


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: IBDC

characteristic: description

text: India

text: India-Jodhpur

text: Urinary tract infection

text: Homo sapiens

text: isolate

characteristic: isolate

text: Urine

text: Escherichia coli

text: Escherichia coli


text: public

characteristic: INSDC status

text: IBDC

characteristic: broker name

characteristic: common name

text: India

characteristic: geographic location (region and locality)

text: Urinary tract infection

text: Homo sapiens

text: isolate

text: Urine

text: Escherichia coli

characteristic: organism

text: Escherichia coli


Upust

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: Upust

tag: Namespace:Senckenberg Biodiversity and Climate Research Centre

text: Lichen-forming fungus

text: Lasallia pustulata

text: Lasallia pustulata

text: Upust

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

tag: Namespace:RIVM - National Institute for Public Health and the Environment

characteristic: Submitter Id

text: CMY-4 postive isolate

text: Netherlands

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: External Id

text: RIVM - National Institute for Public Health and the Environment

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: CTX-M-15 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

characteristic: host scientific name

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


text: public

characteristic: INSDC status

text: CTX-M-55 postive isolate

characteristic: description

text: Netherlands

text: healthy

text: Homo sapiens

characteristic: isolate

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: ENA-CHECKLIST

text: public

text: CTX-M-14 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: ESBL-producing isolate


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: CTX-M-27 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: ENA-LAST-UPDATE

text: public

text: SHV-12 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate

characteristic: title


characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: CMY-2 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


text: public

text: CMY-138 postive isolate

text: Netherlands

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: External Id

characteristic: INSDC center name

text: public

text: DHA-1 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: INSDC first public

text: public

characteristic: collection date

text: CTX-M-65 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


text: public

characteristic: INSDC status

text: DHA-1 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

characteristic: host scientific name

text: Faeces

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: ESBL-producing isolate


text: public

text: SHV-27 postive isolate

characteristic: description

text: Netherlands

text: healthy

text: Homo sapiens

characteristic: isolate

text: Faeces

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: ESBL-producing isolate


characteristic: ENA-CHECKLIST

text: public

text: CTX-M-1 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: ESBL-producing isolate


characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: CTX-M-2 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


characteristic: ENA-LAST-UPDATE

text: public

text: CTX-M-8 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate

characteristic: title


characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: TEM-15 postive isolate

text: Netherlands

text: healthy

text: Homo sapiens

text: Faeces

text: Escherichia coli

text: Escherichia coli

text: ESBL-producing isolate


text: public

text: SHV-106 postive isolate

text: Netherlands

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Homo sapiens

text: Faeces

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: ESBL-producing isolate


E-MTAB-13123:Sample 1

characteristic: ENA first public

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-13123:Sample 1

tag: Namespace:Center for Omics Sciences, IRCCS San Raffaele Hospital

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: Protocols: Fresh tumor specimens obtained from patients with liver metastatic gastrointestinal cancers were used immediately after surgery. Tissues were minced, conditioned in PBS/5mM EDTA and digested in a solution composed of PBS/1mM EDTA, 2X TrypLE™ Select Enzyme and DNAse I for 1h at 37°C. Dissociated cells were collected, resuspended in 120μl growth factor reduced Matrigel™, seeded in single domes in 24-well flat bottom cell culture plate and, after dome solidification, overlaid with 1ml of complete human organoid medium and medium replaced every two/three days. PDOs were dissociated to single cells either for passaging after reaching confluence or for the subsequent downstream applications by mechanical and enzymatic digestion. PDOs were retrieved from Matrigel™ in a solution composed of PBS/1mM EDTA and 1X TrypLE™ Select Enzyme, incubated for 20 min at 37 °C then dissociated to single cells by pipetting. Cells were harvested, resuspended in growth factor reduced Matrigel™ Nucleic acids were directly processed on intact cells following standard Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics) using Chromium platform (10x Genomics). Target cell recovery was 5'000. Libraries were prepared using Chromium Single Cell 3' Reagent v3 chemistry protocol (10X Genomics). Library quality was assessed using TapeStation (Agilent Technologies). Libraries were sequenced on NovaSeq 6000 platform (Illumina) aiming at 50'000 clusters/cell.

text: adult

characteristic: developmental stage

text: colorectal cancer

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not collected

text: organoid

characteristic: growth condition

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: Sample 1


E-MTAB-13123:Sample 2

characteristic: ENA-CHECKLIST

text: Center for Omics Sciences, IRCCS San Raffaele Hospital

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13123:Sample 2

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: colorectal cancer

text: KRAS p.Gly12Ala

text: not collected

text: organoid

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: neoplasm

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-13123:Sample 3

characteristic: ENA first public

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: E-MTAB-13123:Sample 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: adult

text: colorectal cancer

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: organoid

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: neoplasm

text: Homo sapiens

text: Sample 3


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Microomics

characteristic: INSDC first public

text: public

text: environment associated with an animal part or small animal

characteristic: broad-scale environmental context

text: sheep

characteristic: common name

text: vaginal microbiome synchronization day before sponge insertion

text: secretion

characteristic: environmental medium

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: animal-associated environment

characteristic: local environmental context

text: Ovis aries

text: Description of the vaginal microbiota in nulliparous ewes

characteristic: project name

text: Ovis aries


characteristic: ENA-CHECKLIST

text: Microomics

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: collection date

text: sheep

text: vaginal microbiome two days after synchronization

characteristic: description

text: secretion

text: Spain

text: animal-associated environment

text: Ovis aries

characteristic: organism

text: Ovis aries

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Microomics

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: sheep

text: vaginal microbiome after mating

text: secretion

text: Spain

characteristic: geographic location (country and/or sea)

text: animal-associated environment

text: Ovis aries

text: Ovis aries


characteristic: ENA-LAST-UPDATE

text: Microomics

characteristic: INSDC first public

text: public

characteristic: broad-scale environmental context

text: sheep

characteristic: common name

text: vaginal microbiome of after mating

text: secretion

characteristic: environmental medium

text: Spain

characteristic: geographic location (latitude)

text: animal-associated environment

text: Ovis aries

text: Ovis aries


characteristic: ENA-CHECKLIST

text: Microomics

text: public

characteristic: INSDC status

characteristic: SRA accession

text: sheep

text: foreskin microbiome of ram V3 before mating

text: secretion

text: Spain

characteristic: geographic location (longitude)

text: animal-associated environment

characteristic: local environmental context

text: Ovis aries

characteristic: project name

text: Ovis aries


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Microomics

text: public

characteristic: collection date

text: sheep

text: foreskin microbiome of ram V8 before mating

characteristic: description

text: secretion

text: Spain

text: animal-associated environment

text: Ovis aries

characteristic: organism

text: Ovis aries

characteristic: title


characteristic: ENA-LAST-UPDATE

text: Microomics

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: sheep

text: foreskin microbiome of ram R11 before mating

text: secretion

text: Spain

characteristic: geographic location (country and/or sea)

text: animal-associated environment

text: Ovis aries

text: Ovis aries


characteristic: ENA-CHECKLIST

text: Microomics

text: public

characteristic: INSDC status

characteristic: broad-scale environmental context

text: sheep

characteristic: common name

text: foreskin microbiome of ram V3 after mating

text: secretion

characteristic: environmental medium

text: Spain

characteristic: geographic location (latitude)

text: animal-associated environment

text: Ovis aries

text: Ovis aries


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Microomics

text: public

characteristic: SRA accession

text: sheep

text: foreskin microbiome of ram V8 after mating

text: secretion

text: Spain

characteristic: geographic location (longitude)

text: animal-associated environment

characteristic: local environmental context

text: Ovis aries

characteristic: project name

text: Ovis aries


characteristic: ENA-LAST-UPDATE

text: Microomics

characteristic: INSDC center name

text: public

characteristic: collection date

text: sheep

text: foreskin microbiome of ram R11 after mating

characteristic: description

text: secretion

text: Spain

text: animal-associated environment

text: Ovis aries

characteristic: organism

text: Ovis aries

characteristic: title


characteristic: ENA-CHECKLIST

text: Curtin University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-10-07-2023-09:09:07:871-65953

tag: Namespace:Curtin University

characteristic: Submitter Id

text: Cyp51A amplicon sequences from a mix of genomic DNA from seven P. teres isolates

text: Australia

characteristic: geographic location (country and/or sea)

text: Pyrenophora teres

text: Pyrenophora teres


characteristic: ENA first public

characteristic: External Id

text: Research Centre for the Humanities

text: public

tag: Namespace:Research Centre for the Humanities

text: human

characteristic: common name

text: complete mitochondrial sequence, Hungarian from Baranja

text: Croatia

text: Homo sapiens

text: Homo sapiens


text: Research Centre for the Humanities

text: public

characteristic: SRA accession

text: human

text: complete mitochondrial sequence, Hungarian from Zobor region

text: Slovakia

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: GSC

text: public

text: France

text: [Candida] anglica

text: [Candida] anglica

characteristic: strain


characteristic: ENA-LAST-UPDATE

text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

characteristic: INSDC center name

text: public

tag: Namespace:ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: human

text: COLO 829BL cell line sample sequenced at high depth on Illumina NovaSeq

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

characteristic: collection date

text: human

text: COLO 829BL cell line samples equenced at high depth on Illumina NextSeq

characteristic: description

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: COLO 829BL cell line sample sequenced at low depth on Illumina NovaSeq

text: USA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

characteristic: INSDC first public

text: public

text: human

text: COLO 829BL cell line samples equenced at low depth on Illumina NextSeq

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: 697 cancer cell line from childhood B acute lymphoblastic leukemia

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

characteristic: Submitter Id

text: human

text: EW-8 cancer cell line from Ewing sarcoma

text: USA

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens


characteristic: External Id

text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: GM12878 non-cancer cell line

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

characteristic: common name

text: K562 cancer cell line from Chronic myeloid leukemia

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

characteristic: SRA accession

text: human

text: ME-1 cancer cell line from Human myeloma

text: USA

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: Molm13 cancer cell line from Acute myeloid leukemia

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: Rh30 cancer cell line from Alveolar rhabdomyosarcoma

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 10% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 10% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 5% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 5% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 2.5% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 2.5% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 1% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 1% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.5% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.5% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.2% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.2% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.1% cancer cell lines dilution sample replicate A

text: USA

text: Homo sapiens

text: Homo sapiens


text: ST. JUDE CHILDREN'S RESEARCH HOSPITAL

text: public

text: human

text: 0.1% cancer cell lines dilution sample replicate B

text: USA

text: Homo sapiens

text: Homo sapiens


text: CHRISTIAN MEDICAL COLLEGE

text: public

tag: Namespace:CHRISTIAN MEDICAL COLLEGE

text: Genome Surveillance of K. pneumoniae from livestock specimens and hospital sewage

text: India

characteristic: investigation type

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: open sewer line

characteristic: sewage type


characteristic: ENA-LAST-UPDATE

text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC center name

text: public

text: India

text: Klebsiella quasipneumoniae subsp. similipneumoniae

text: open sewer line


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: collection date

characteristic: description

text: India

text: Klebsiella quasipneumoniae

text: Klebsiella quasipneumoniae

text: open sewer line


text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

characteristic: host health state

text: Bos taurus

characteristic: host scientific name

characteristic: isolate

text: Intestine

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

characteristic: title


characteristic: ENA-CHECKLIST

text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: India

text: healthy

text: Bos taurus

text: Tissue


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: SRA accession

text: India

characteristic: geographic location (country and/or sea)

text: healthy

text: Bos taurus

text: Tissue

text: Klebsiella variicola subsp. variicola

text: Klebsiella variicola subsp. variicola


characteristic: ENA-LAST-UPDATE

text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC center name

text: public

text: India

text: healthy

text: Bos taurus

text: Tissue

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: collection date

characteristic: description

text: India

text: healthy

text: Gallus domesticus

text: Intestine

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

characteristic: host health state

text: Gallus domesticus

characteristic: host scientific name

text: Intestine


text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

text: Gallus domesticus

characteristic: isolate

text: Tissue

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


characteristic: ENA-CHECKLIST

text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

text: Vertebrata (subphylum)

text: Intestine

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: title


text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: India

text: healthy

text: Vertebrata (subphylum)

text: Tissue

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: India

text: diseased

text: Homo sapiens

text: Blood

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: diseased

text: Homo sapiens

text: Blood


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: SRA accession

text: India

characteristic: geographic location (country and/or sea)

text: healthy

text: Capra hircus

text: Intestine

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: ENA-LAST-UPDATE

text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC center name

text: public

text: India

text: healthy

text: Capra hircus

text: Intestine


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: collection date

characteristic: description

text: India

text: healthy

text: Capra hircus

text: Tissue

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

characteristic: host health state

text: Capra hircus

characteristic: host scientific name

text: Tissue


text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

text: Sus domesticus

characteristic: isolate

text: Intestine

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


characteristic: ENA-CHECKLIST

text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

text: Sus domesticus

text: Intestine

characteristic: title


text: CHRISTIAN MEDICAL COLLEGE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: India

text: healthy

text: Sus domesticus

text: Intestine

text: Klebsiella quasipneumoniae

text: Klebsiella quasipneumoniae


text: CHRISTIAN MEDICAL COLLEGE

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: India

text: healthy

text: Sus domesticus

text: Tissue

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: CHRISTIAN MEDICAL COLLEGE

text: public

text: India

text: healthy

text: Sus domesticus

text: Tissue


text: Rothamsted Research

text: public

characteristic: SRA accession

tag: Namespace:Rothamsted Research

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Fusarium graminearum PH-1

text: Fusarium graminearum PH-1


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

text: public

tag: Namespace:GFZ German Research Centre for Geosciences

text: Plastic soil time point 1

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 1


tag: attribute

text: GFZ German Research Centre for Geosciences

text: public

characteristic: collection date

text: Plastic soil time point 5

characteristic: description

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 5


text: public

text: Forest soil time point 1

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 1


text: public

text: Forest soil time point 5

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 5


text: public

text: Forest soil time point 1 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 1 Glass 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 1 Glass 2


text: public

text: Forest soil time point 1 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 1 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 1 Plastic 2


text: public

text: Forest soil time point 2 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 2 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 2 Plastic 2


text: public

text: Forest soil time point 3 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 3 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 3 Plastic 2


text: public

text: Forest soil time point 5 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 5 Glass 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 5 Glass 2


text: public

text: Forest soil time point 5 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 5 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Forest soil 5 Plastic 2


text: public

text: Plastic soil time point 1 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 1 Glass 1


text: public

text: Plastic soil time point 1 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 1 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 1 Plastic 2


text: public

text: Plastic soil time point 2 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 2 Glass 2


text: public

text: Plastic soil time point 2 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 2 Plastic 2


text: public

text: Plastic soil time point 3 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 3 Glass 2


text: public

text: Plastic soil time point 3 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 3 Plastic 2


text: public

text: Plastic soil time point 5 incubated with glass

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 5 Glass 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 5 Glass 2


text: public

text: Plastic soil time point 5 incubated with plastic

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 5 Plastic 1


text: public

text: Germany

text: soil metagenome

text: soil metagenome

text: Plastic soil 5 Plastic 2


text: CIPH

text: public

text: Croatia

text: Homo Sapiens

characteristic: host scientific name

text: Campylobacter jejuni

text: Campylobacter jejuni


text: Queen's University Belfast

text: public

tag: Namespace:Queen's University Belfast

text: Dr Paul McCusker

text: liver fluke

characteristic: common name

text: Control juvenile F. hepatica maintained in vitro for 22 days replicate 1

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)

characteristic: strain


characteristic: ENA-CHECKLIST

text: Queen's University Belfast

text: public

text: Dr Paul McCusker

text: liver fluke

text: Control juvenile F. hepatica maintained in vitro for 22 days replicate 2

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

characteristic: organism

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)


text: Queen's University Belfast

characteristic: INSDC first public

text: public

text: Dr Paul McCusker

text: liver fluke

text: Control juvenile F. hepatica maintained in vitro for 22 days replicate 3

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)

characteristic: title


text: Queen's University Belfast

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Dr Paul McCusker

text: liver fluke

text: Juveniles in vitro F. hepatica that were treated with 200 grays of radiation on day 20 before further maintance until day 22 replicate 1

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)


characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

characteristic: Submitter Id

text: Dr Paul McCusker

text: liver fluke

text: Juveniles in vitro F. hepatica that were treated with 200 grays of radiation on day 20 before further maintance until day 22 replicate 2

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)


characteristic: External Id

text: Queen's University Belfast

text: public

characteristic: SRA accession

text: Dr Paul McCusker

text: liver fluke

text: Juveniles in vitro F. hepatica that were treated with 200 grays of radiation on day 20 before further maintance until day 22 replicate 3

text: Juvenile

text: United Kingdom

text: Fasciola hepatica

text: Fasciola hepatica

text: Italian (Ridgeway Research Ltd)


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF SZEGED

text: public

tag: Namespace:UNIVERSITY OF SZEGED

text: 12h p.i. Peracetic acid (PAA) treated PRV infection

text: Hungary

characteristic: geographic location (country and/or sea)

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

characteristic: INSDC center name

text: public

characteristic: collection date

text: 1h p.i. Peracetic acid (PAA) treated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 2h p.i. Peracetic acid (PAA) treated PRV infection

characteristic: description

text: Hungary

text: Sus scrofa

characteristic: host scientific name

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 4h p.i. Peracetic acid (PAA) treated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 6h p.i. Peracetic acid (PAA) treated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 8h p.i. Peracetic acid (PAA) treated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 12h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 1h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 2h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 4h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 6h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: UNIVERSITY OF SZEGED

text: public

text: 8h p.i. untreated PRV infection

text: Hungary

text: Sus scrofa

text: Suid herpesvirus 1 strain Kaplan

text: Suid herpesvirus 1 strain Kaplan


text: Tel Hai College

text: public

tag: Namespace:Tel Hai College

text: not provided

text: DEW

text: Israel

text: Triticum turgidum subsp. dicoccum

text: Triticum turgidum subsp. dicoccum


text: EMBL

text: public

text: E-MTAB-13271:scyl-chrb_MID-LA_DEL_Rep1_left

text: 3 to 18

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: fruit fly

characteristic: common name

text: Protocols: Wildtype flies were held in population cages at 25ºC. After three one-hour pre-lays, embryos were collected at the indicated time (please see age) after egg laying. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at room temperature for 15 minutes. The reaction was terminated with ice-cold 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. 0.5-1 g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-µm Sefar Nitex membrane. The total number of nuclei was determined using a flow cytometer or cell counter. Four aliquots of 25 million nuclei were used for preparation of the 3C library for each sample. 3C samples and Capture-C libraries were prepared as previously described (Davies et al. 2016, Ghavi-Helm et al., 2019), using DpnII as restriction enzyme and performing the ligation step in nucleus. The template was then processed with the Roche Nimblegen SeqCap EZ Library SR system and a double capture strategy.

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

characteristic: genotype

text: not collected

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13271:scyl-chrb_MID-LA_DEL_Rep1_right

characteristic: Submitter Id

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

characteristic: title


text: EMBL

characteristic: INSDC center name

text: public

text: E-MTAB-13271:scyl-chrb_MID-LA_DEL_Rep2_left

text: 3 to 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

characteristic: INSDC first public

text: public

text: E-MTAB-13271:scyl-chrb_MID-LA_DEL_Rep2_right

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain


text: EMBL

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13271:scyl-chrb_scyl_DEL_Rep1_left

characteristic: Submitter Id

text: 3 to 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

text: normal

text: deletion

text: w;;scyl-deletion

text: not collected

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-13271:scyl-chrb_scyl_DEL_Rep1_right

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

text: w;;scyl-deletion

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13271:scyl-chrb_scyl_DEL_Rep2_left

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

text: normal

text: deletion

text: w;;scyl-deletion

text: not collected

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-13271:scyl-chrb_scyl_DEL_Rep2_right

characteristic: Submitter Id

text: 3 to 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

text: normal

text: deletion

text: w;;scyl-deletion

text: not collected

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

characteristic: title


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13271:scyl-chrb_scyl-LA_DEL_Rep1_left

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

characteristic: SRA accession

text: E-MTAB-13271:scyl-chrb_scyl-LA_DEL_Rep1_right

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13271:scyl-chrb_scyl-LA_DEL_Rep2_left

characteristic: Submitter Id

text: 3 to 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-13271:scyl-chrb_scyl-LA_DEL_Rep2_right

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13271:tsh-tio_MID-LA_DEL_Rep1_left

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

characteristic: initial time point

text: not applicable

characteristic: isolate

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: E-MTAB-13271:tsh-tio_MID-LA_DEL_Rep1_right

characteristic: Submitter Id

text: 3 to 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: fruit fly

text: normal

text: deletion

text: not collected

text: egg laying

text: not applicable

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

characteristic: title


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13271:tsh-tio_MID-LA_DEL_Rep2_left

text: 3 to 18

text: ArrayExpress

text: not collected

text: fruit fly

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: deletion

characteristic: genetic modification

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: egg laying

text: not applicable

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed