text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Control 2hr rep2


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DPSQ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Z. parabailii (strain ATCC 60483) RNA sample

characteristic: description

text: Zygosaccharomyces parabailii

characteristic: organism

text: Zygosaccharomyces parabailii

text: ATCC 60483

characteristic: strain

text: Control 2hr rep3

characteristic: title


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Glabridin 2hr rep1


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Glabridin 2hr rep2


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Glabridin 2hr rep3


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Wighteone 2hr rep1


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Wighteone 2hr rep2


text: DPSQ

text: public

text: Zygosaccharomyces parabailii

text: Zygosaccharomyces parabailii

text: ATCC 60483

text: Wighteone 2hr rep3


text: IDIBELL

text: public

characteristic: collection date

text: Blood

text: Spain

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Blood

text: Streptococcus dysgalactiae subsp. equisimilis

text: ND

characteristic: serovar


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IDIBELL

text: public

text: Blood

text: Spain

text: diseased

text: Homo sapiens

text: Blood

text: 43.292405_ -1.97047

text: ND


text: AALBORG UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78619

tag: Namespace:AALBORG UNIVERSITY

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78620

characteristic: Submitter Id

characteristic: description

text: uncultured bacterium

characteristic: organism

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78621

text: uncultured bacterium

text: uncultured bacterium

characteristic: title


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78622

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78623

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78624

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78625

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78626

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78627

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78628

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78629

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78630

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78631

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-07:58:57:579-78632

text: uncultured bacterium

text: uncultured bacterium


text: AALBORG UNIVERSITY

text: public

text: ena-SAMPLE-TAB-08-09-2022-08:57:06:812-78692

text: anaerobic digester metagenome

text: anaerobic digester metagenome

text: Metagenome


text: Barts Cancer Institute

text: public

tag: Namespace:Barts Cancer Institute

text: human

characteristic: common name

text: Targeted sequencing of human DNA from vial x7892

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F8757

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F8903

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F9141

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F9056

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F9681

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial F9788

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R3054

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R3455

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R3730

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R5278

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R5150

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R6490

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R6171

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R6275

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R6679

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R7026

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R6357

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R7773

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R9089

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R9090

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R9150

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R9527

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R9605

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T0990

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T1225

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T1663

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T1809

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T2353

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T2410

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T1929

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T1553

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T5062

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T5306

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T5656

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T5896

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T6083

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T5876

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T6391

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T6733

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T6810

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T7714

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T7880

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T8169

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T8401

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T8725

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T8769

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T8546

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C0210

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C0982

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C1099

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C1520

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C1706

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C1568

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial R8712

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial T6033

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Barts Cancer Institute

text: public

text: human

text: Targeted sequencing of human DNA from vial C0912

text: Homo sapiens

text: Homo sapiens

text: Targeted sequencing of human DNA


text: Teagasc Food Research Centre

text: public

tag: Namespace:Teagasc Food Research Centre

text: Hafnia Paralvei isolated from milk

text: Milk

text: milk metagenome

text: milk metagenome

text: H. Paralvei 1


text: Teagasc Food Research Centre

text: public

text: Hafnia Paralvei isolated from milk

text: Milk

text: milk metagenome

text: milk metagenome

text: H. Paralvei 2


text: Teagasc Food Research Centre

text: public

text: Hafnia Paralvei isolated from milk

text: Milk

text: milk metagenome

text: milk metagenome

text: H. Paralvei 3


text: Teagasc Food Research Centre

text: public

text: Hafnia Paralvei isolated from milk

text: Milk

text: milk metagenome

text: milk metagenome

text: H. Paralvei 4


text: Teagasc Food Research Centre

text: public

text: Hafnia Paralvei isolated from milk

text: Milk

text: milk metagenome

text: milk metagenome

text: H. Paralvei 5


text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium  VIB Center for Plant Systems Biology, VIB, Gent, Belgium

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: After around 35 days of growth all stage 12c flowers on the main stem were emasculated and harvested after 2, 3, or 4 days. Unpollinated pistils of emasculated wild-type flowers were dissected as described previously. For each time point the ovules of over 75 pistils (approximately 4000 ovules) were collected on dry ice with the help of a vacuum-driven micro-aspirator (Sanchez-Leon et al., 2012). The whole time series was sampled in three independent batches (four time points in each round, 2 to 4 DAE). Arabidopsis seeds (Columbia-0, Col-0) were sown on Jiffy-7C propagation plugs (Jiffy) and stratified for two to three days at 4 °C. Plants were grown for about 35 days at 22°C under a 16 h light/8 h dark regime before being emasculated. After subsequent tissue grinding, RNA was extracted with the Spectrum Plant Total RNA kit (Sigma). RNA quantity and quality was assessed by spectrophotometric analysis (NanoDrop ND-2000, Thermo) and on-chip electrophoresis (RNA 6000 Nano Kit, Agilent). Library preparation was done using the TruSeq unstranded RNA Sample Preparation Kit v2 (Illumina).

text: mature non-fertilized ovule

characteristic: developmental stage

characteristic: ecotype

text: wild type genotype

characteristic: genotype

text: not applicable

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: plant ovule

characteristic: organism part

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium  VIB Center for Plant Systems Biology, VIB, Gent, Belgium

text: public

text: ArrayExpress

text: thale cress

text: mature non-fertilized ovule

text: wild type genotype

text: not applicable

characteristic: isolate

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: plant ovule

text: Arabidopsis thaliana


characteristic: External Id

text: UNIVERSITY OF COPNEHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:UNIVERSITY OF COPNEHAGEN

characteristic: collection date

text: TraDIS in MG1655/pTF2

text: Denmark

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: host health state

text: not applicable

characteristic: host scientific name

text: E. coli

text: not applicable

text: Escherichia coli

text: Escherichia coli

text: TraDIS in MG1655/pTF2


text: WW0591/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: SRA accession

text: Department of Endocrinology, Diabetes and Metabolism, University Children's Hospital, University Medical Centre Ljubljana

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

tag: Namespace:National Institute of Biology

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Ljubljana 1

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0591/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

text: INEXTVIR -20

text: Sequenced wastewater sample from Central WWTP Ljubljana 2

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

text: Illumina

text: wastewater/sludge


text: WW0595/22 P-EL

text: National Institute of Biology

text: public

characteristic: SRA accession

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Koper 1

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: organism

characteristic: project name

text: Illumina

characteristic: sequencing method

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0595/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

text: INEXTVIR -20

text: Sequenced wastewater sample from Central WWTP Koper 2

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

text: Illumina

text: wastewater/sludge


text: WW0599/22 P-EL

text: National Institute of Biology

text: public

characteristic: SRA accession

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Maribor 1

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: organism

characteristic: project name

text: Illumina

characteristic: sequencing method

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0599/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

text: INEXTVIR -20

text: Sequenced wastewater sample from Central WWTP Maribor 2

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

text: Illumina

text: wastewater/sludge


text: Anopheles gambiae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: African malaria mosquito

characteristic: common name

text: Anopheles gambiae

characteristic: organism

text: Anopheles gambiae

characteristic: title


text: WW0563/21 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: National Institute of Biology

text: public

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0563/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0567/21 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: National Institute of Biology

text: public

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0567/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0571/21 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: National Institute of Biology

text: public

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

characteristic: description

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0571/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: Forward file name

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: No. replicate

characteristic: Reverse file name

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

characteristic: geographic location (country and/or sea)

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


E-MTAB-12191:si-control Laminar 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12191:si-control Laminar 1

tag: Namespace:Queen Mary University of London; William Harvey Research Institute, Centre of Cardiovascular Medicine and Device

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: common name

text: Protocols: HUVECs transfected with siRNA targeting NRP1 or with a non-targeting siRNA were cultured in static conditions or exposed to laminar or oscillatory flow for 24 hours. RNAs from 3 independent experiments were isolated using the protocol described below and transcriptomic analysis performed by Novogene, UK. mRNA was collected using the Monarch® Total RNA Miniprep Kit (New England BioLabs, UK; cat#: T2010S) and cDNA was prepared using LunaScript® RT SuperMix Kit (New England BioLabs, UK; cat#: E3010L). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X) or by using sonication with Diagenode bioruptor Pico for breaking RNA strands. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: laminar flow

characteristic: environmental stress

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

characteristic: organism part

text: Homo sapiens

text: si-control Laminar 1


E-MTAB-12191:si-control Laminar 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen Mary University of London; William Harvey Research Institute, Centre of Cardiovascular Medicine and Device

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12191:si-control Laminar 2

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: laminar flow

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Laminar 2


E-MTAB-12191:si-control Laminar 3

text: public

characteristic: SRA accession

text: E-MTAB-12191:si-control Laminar 3

characteristic: Submitter Id

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: laminar flow

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Laminar 3

characteristic: title


E-MTAB-12191:si-control Oscillatory 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12191:si-control Oscillatory 1

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: common name

text: neonate

text: normal

text: oscillatory flow

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Oscillatory 1


E-MTAB-12191:si-control Oscillatory 2

text: public

text: E-MTAB-12191:si-control Oscillatory 2

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: oscillatory flow

characteristic: environmental stress

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Oscillatory 2


E-MTAB-12191:si-control Oscillatory 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12191:si-control Oscillatory 3

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: oscillatory flow

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

characteristic: organism part

text: Homo sapiens

text: si-control Oscillatory 3


E-MTAB-12191:si-control Static 1

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12191:si-control Static 1

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: static

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Static 1


E-MTAB-12191:si-control Static 2

text: public

characteristic: SRA accession

text: E-MTAB-12191:si-control Static 2

characteristic: Submitter Id

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: static

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Static 2

characteristic: title


E-MTAB-12191:si-control Static 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12191:si-control Static 3

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: common name

text: neonate

text: normal

text: static

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-control Static 3


E-MTAB-12191:si-NRP1 Laminar 1

text: public

text: E-MTAB-12191:si-NRP1 Laminar 1

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: laminar flow

characteristic: environmental stress

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 Laminar 1


E-MTAB-12191:si-NRP1 Laminar 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12191:si-NRP1 Laminar 2

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: laminar flow

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

characteristic: organism part

text: Homo sapiens

text: si-NRP1 Laminar 2


E-MTAB-12191:si-NRP1 Laminar 3

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12191:si-NRP1 Laminar 3

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: laminar flow

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 Laminar 3


E-MTAB-12191:si-NRP1 Oscillatory 1

text: public

characteristic: SRA accession

text: E-MTAB-12191:si-NRP1 Oscillatory 1

characteristic: Submitter Id

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: oscillatory flow

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 Oscillatory 1

characteristic: title


E-MTAB-12191:si-NRP1 Oscillatory 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12191:si-NRP1 Oscillatory 2

text: ArrayExpress

characteristic: broker name

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: common name

text: neonate

text: normal

text: oscillatory flow

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 Oscillatory 2


E-MTAB-12191:si-NRP1 Oscillatory 3

text: public

text: E-MTAB-12191:si-NRP1 Oscillatory 3

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

characteristic: description

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: oscillatory flow

characteristic: environmental stress

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 Oscillatory 3


E-MTAB-12191:si-NRP1 static 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12191:si-NRP1 static 1

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: static

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

characteristic: organism part

text: Homo sapiens

text: si-NRP1 static 1


E-MTAB-12191:si-NRP1 static 2

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12191:si-NRP1 static 2

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: static

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 static 2


E-MTAB-12191:si-NRP1 static 3

text: public

characteristic: SRA accession

text: E-MTAB-12191:si-NRP1 static 3

characteristic: Submitter Id

text: ArrayExpress

text: HUVEC cell line

text: endothelial cell of umbilical vein

text: human

text: neonate

text: normal

text: static

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: umbilical vein

text: Homo sapiens

text: si-NRP1 static 3

characteristic: title


text: WW0536/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0536/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0538/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0538/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0546/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0546/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0511/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Domzale Kamnik 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0511/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Domzale Kamnik 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0513/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0513/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0521/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: ENA-FIRST-PUBLIC

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0521/22 p-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: DNA concentration (Qubit)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

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text: wastewater treatment plant influent

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text: wastewater treatment plant influent

text: Slovenia

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text: Illumina

characteristic: title

text: wastewater/sludge


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text: public

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characteristic: Storage location at NIB

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characteristic: environment (biome)

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: investigation type

characteristic: project name

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characteristic: sequencing method

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characteristic: Cq (N1)

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

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characteristic: INSDC last update

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characteristic: INSDC status

characteristic: SRA accession

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characteristic: Submitter Id

characteristic: description

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characteristic: title

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characteristic: Forward file name

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text: public

characteristic: No. replicate

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text: wastewater treatment plant influent

characteristic: environment (biome)

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text: wastewater treatment plant influent

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: investigation type

characteristic: project name

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characteristic: sequencing method

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characteristic: wastewater/sludge environmental package


text: WW0487/21 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

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text: wastewater treatment plant influent

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0495/21 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

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characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

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characteristic: SRA accession

text: INEXTVIR -20

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text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

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text: virus

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text: Illumina

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text: wastewater/sludge


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

characteristic: collection date

text: H37Rv lab strain

text: South Africa

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Mtb

characteristic: isolate

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

text: public

text: resistant mutant

text: South Africa

text: diseased

text: Homo sapiens

text: Mtb

text: Sputum

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France

text: ArrayExpress

characteristic: broker name

text: Protocols: Following a shift at 37°C (duration depends on the mutant), after reaching exponential phase at 25°C in YPD, cells were cross-linked with 1% formaldehyde during 10 minutes. Cells were grown exponentially to 0.6 OD600 and cross-linked with 1% formaldehyde for 10 min. They were then washed with ST buffer (10 mM Tris-Cl pH 7.5, 100 mM NaCl) and frozen. Cells were lysed by bead-beating in FA lysis buffer (50 mM Hepes-KOH pH 8, 150 mM NaCl, 0.5 mM EDTA, 1% Triton, 0.1% sodium deoxycholate) supplemented with PMSF for 30 minutes at 4°C. Chromatin was recovered after a centrifuge step (16,000 rcf, 10 min, 4°C) in MNase buffer (20 mM Tris-HCl pH 7.5, 0.34 M sucrose, 15 mM KCl, 60 mM NaCl, 3 mM CaCl2) and was subjected to mild MNase (NEB, M0247S) treatment (20 min, 37°C on thermomixer). Reaction was stopped by addition of 10 mM EDTA on ice. Digested chromatin was recovered after centrifugation (16,000 rcf, 10 min, 4°C), and the remaining pellet was mildly sonicated (20” ON + 40” OFF, 4 cycles, mild), after a centrifugation step under similar conditions the chromatin samples were recovered at -80°C. The sizes of the DNA fragments have been checked by migrating the samples on both hand-made agarose and BioAanalyzer (Agilent) after pronase treatment. DNA was extracted with PCR purification kit (Qiagen). DNA was extracted using the Auto iPure V2 kit from Diagenode, following the manufacturer recommendations. Library construction was done according to the takara SMARTER thruplex (takara bio) protocol, following manufacturer's recommendation. Libraries were sized with AMPure beads (Beckman-coulter) to a final size of 325bp.

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 MED17:CEN:TRP1 RSC8:13MYC:KANMX

characteristic: genotype

text: Shift at 37°C during 45min

characteristic: growth condition

text: RPM

characteristic: normalization

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12198:IP-Myc_Med14-Myc_2h30-shift

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6

text: Shift at 37°C during 2h30

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Shift at 37°C during 6h

text: Spike-in

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6 rsc8-ts21 (G326D, I417F, K446M)::KanR

text: Shift at 37°C during 6h

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6 sth1-ts (P646L, F655L, D657G ,N1077S,F1125L)

text: Shift at 37°C during 2h30

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: External Id

text: public

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 RSC8::13MYC::KAN::LEU2

text: Shift at 37°C during 2h30

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: INSDC center name

text: public

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 RSC8::13MYC::KAN::LEU2 sth1-ts( P646L F655L , D657G ,N1077S,F1125L)

text: Shift at 37°C during 2h30

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

characteristic: broker name

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 STH1::13MYC::KAN::LEU2

text: Shift at 37°C during 6h

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 med17-140:CEN:TRP1 STH1:13MYC:KANMX

characteristic: genotype

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 med17-444:CEN:TRP1 STH1:13MYC:KANMX

text: Shift at 37°C during 45min

characteristic: growth condition

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 MED17:CEN:TRP1 STH1:13MYC:KANMX

text: Shift at 37°C during 45min

text: Spike-in

characteristic: normalization

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: INSDC first public

text: public

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Dmed17::kan::ADE2 MED17 CEN URA3 STH1::13MYC::KAN::LEU2 rsc8-ts21(G326D, I417F, K446M)::KanR

text: Shift at 37°C during 6h

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: INSDC last update

text: public

text: E-MTAB-12198:IP-Pol2_Med14-Myc_2h30-shift

text: ArrayExpress

text: Shift at 37°C during 2h30

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

characteristic: INSDC status

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED14Myc HIS CEN med17-140 TRP

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

characteristic: SRA accession

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED14Myc HIS CEN med17-444 TRP

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: Following a shift at 37°C (duration depends on the mutant), after reaching exponential phase at 25°C in YPD, cells were cross-linked with 1% formaldehyde during 10 minutes. Cells were grown exponentially to 0.6 OD600 and cross-linked with 1% formaldehyde for 10 min. They were then washed with ST buffer (10 mM Tris-Cl pH 7.5, 100 mM NaCl) and frozen. Cells were lysed by bead-beating in FA lysis buffer (50 mM Hepes-KOH pH 8, 150 mM NaCl, 0.5 mM EDTA, 1% Triton, 0.1% sodium deoxycholate) supplemented with PMSF for 30 minutes at 4°C. Chromatin was recovered after a centrifuge step (16,000 rcf, 10 min, 4°C) in MNase buffer (20 mM Tris-HCl pH 7.5, 0.34 M sucrose, 15 mM KCl, 60 mM NaCl, 3 mM CaCl2) and was subjected to mild MNase (NEB, M0247S) treatment (20 min, 37°C on thermomixer). Reaction was stopped by addition of 10 mM EDTA on ice. Digested chromatin was recovered after centrifugation (16,000 rcf, 10 min, 4°C), and the remaining pellet was mildly sonicated (20” ON + 40” OFF, 4 cycles, mild), after a centrifugation step under similar conditions the chromatin samples were recovered at -80°C. The sizes of the DNA fragments have been checked by migrating the samples on both hand-made agarose and BioAanalyzer (Agilent) after pronase treatment. DNA was extracted with PCR purification kit (Qiagen). DNA was extracted using the Auto iPure V2 kit from Diagenode, following the manufacturer recommendations. Library construction was done according to the takara SMARTER thruplex (takara bio) protocol, following manufacturer's recommendation. Libraries were sized with AMPure beads (Beckman-coulter) to a final size of 325bp.

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED14Myc HIS CEN MED17 TRP

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France

text: public

text: E-MTAB-12198:MNase_input_Med14-Myc_2h30-shift

text: ArrayExpress

characteristic: description

text: Shift at 37°C during 2h30

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12198:MNase_input_Med14-Myc_6h-shift

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6

text: Shift at 37°C during 6h

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: E-MTAB-12198:MNase_input_Med14-Myc_rsc8-ts

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6 rsc8-ts21 (G326D, I417F, K446M)::KanR

text: Shift at 37°C during 6h

text: RPM

text: Saccharomyces cerevisiae S288C

characteristic: organism

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: E-MTAB-12198:MNase_input_Med14-Myc_sth1-ts

text: ArrayExpress

text: MATa ura3-52 his3-D200 ade2-101uaa trp1-D63 lys2-801uag leu2-D1 Δmed17::kan::ADE2 MED17 CEN URA3 MED14::13myc::HIS3MX6 sth1-ts (P646L, F655L, D657G ,N1077S,F1125L)

text: Shift at 37°C during 2h30

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12198:MNase_input_Rsc8-Myc_med17-140

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 med17-140:CEN:TRP1 RSC8:13MYC:KANMX

text: Shift at 37°C during 45min

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12198:MNase_input_Rsc8-Myc_med17-444

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 med17-444:CEN:TRP1 RSC8:13MYC:KANMX

text: Shift at 37°C during 45min

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: External Id

text: public

text: ArrayExpress

text: MATa ura3-52 his3-∆200 ade2-101uaa trp1-∆63 lys2-801uag leu2-∆1 ∆med17::kan::ADE2 MED17:CEN:TRP1 RSC8:13MYC:KANMX

text: Shift at 37°C during 45min

text: RPM

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


characteristic: INSDC center name

text: public

text: ArrayExpress

text: MATa ade2-1 lys2-801 ura3-52 trp1-∆63 his3-∆200 leu2∆

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

characteristic: broker name

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

characteristic: genotype

text: Shift at 37°C during 45min

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: public

text: ArrayExpress

text: Shift at 37°C during 45min

characteristic: growth condition

text: Spike-in

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C

text: Saccharomyces cerevisiae S288C


text: Anopheles gambiae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: African malaria mosquito

characteristic: common name

text: Anopheles gambiae

text: Anopheles gambiae


text: Plasmodium falciparum

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: Universita degli studi di Milano

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Universita degli studi di Milano

text: Name_Condition_Treatment_Visit_ClinicalResponse

text: bacterium

text: bacterium


text: public

tag: Namespace:Fraunhofer Institute for Molecular Biology and Applied Ecology IME

characteristic: Submitter Id

unit: hour

characteristic: age

text: ArrayExpress

text: zebrafish

text: Protocols: Ethinylestradiol (CAS: 57-63-6) was purchased from Merck KGgA (Darmstadt, Germany). For the test solution preparation, first a high concentrated stock solution was prepared in water. From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binocular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 ± 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. Total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adapter sequences were removed using trimmomatic (v0.39) and library’s sequence quality was assessed with FastQC (v0.11.5). Reads were checked for potential contaminations with FastQ Screen (v0.14.1) using bowtie2 (v2.3.2) against the following genomes: Daphnia magna (ftp://ftp.ensemblgenomes.org/pub/metazoa/release-48/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz), Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Eschericia coli as well as custom build human rRNA database. With the exception of D. magna, pre-built Bowtie2 indices for those genomes were directly downloaded from Babraham Bioinformatics with the built-in function ‘fastq_screen --get_genomes’.

characteristic: description

text: larval stage

characteristic: developmental stage

text: wild type genotype

text: mixed pool of 10 larvae

characteristic: individual

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: mixed

characteristic: sex

text: AB

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Fraunhofer Institute for Molecular Biology and Applied Ecology IME

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: zebrafish

text: larval stage

text: wild type genotype

text: mixed pool of 10 larvae

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

text: Danio rerio

text: mixed

text: AB

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: zebrafish

characteristic: common name

text: Protocols: Tamoxifen (CAS: 10540-29-1) was purchased from Merck KGgA (Darmstadt, Germany). For the test solution preparation, first a high concentrated stock solution was prepared in water. From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binocular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 ± 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. Total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adapter sequences were removed using trimmomatic (v0.39) and library’s sequence quality was assessed with FastQC (v0.11.5). Reads were checked for potential contaminations with FastQ Screen (v0.14.1) using bowtie2 (v2.3.2) against the following genomes: Daphnia magna (ftp://ftp.ensemblgenomes.org/pub/metazoa/release-48/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz), Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Eschericia coli as well as custom build human rRNA database. With the exception of D. magna, pre-built Bowtie2 indices for those genomes were directly downloaded from Babraham Bioinformatics with the built-in function ‘fastq_screen --get_genomes’.

text: larval stage

text: wild type genotype

characteristic: genotype

text: mixed pool of 10 larvae

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: mixed

text: AB


text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: zebrafish

text: Protocols: Methyltestosterone (CAS: 58-18-4) was purchased from Merck KGgA (Darmstadt, Germany). For the test solution preparation, first a high concentrated stock solution was prepared in water. From this stock, respective volumes for each testing concentration were added to a 250 ml DURAN glass bottle. Then 200 ml of Cu reduced water were added and solutions were stirred in the dark for 3 hours at room temperature. The solutions were freshly prepared one day prior the start of the experiment and stored at room temperature. They were constantly aerated and used over the course of the 96 hours exposure experiment. The glass wells for the incubation of the embryos were pre-saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample, about 40 - 50 fertilized fish eggs were pre-picked in glass petri dishes (10 cm diameter) filled with 30 ml of the testing solution. Using an optical binocular microscope, 15 embryos of the same early blastula stage were transferred from the pre-picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Adult animal husbandry: Wild-type zebrafish (Danio rerio, Strain AB) broodstocks were maintained under flow-through conditions in 150 L tanks at 26 +/- 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® (Tetra Werke, Melle, Germany) main feed ad libitum and nauplii of Artemia salina. The day before test start, glass spawning-trays with artificial substrate (green glass beads stringed on stainless steel wire) were placed at the bottom of each tank. After mating and spawning in the morning hours eggs were rinsed with clear Cu-reduced water and placed into glass dishes for pre-picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes (diameter 6 cm) filled with 8 ml of the respective testing solution (Control, Low exposure, High exposure). Embryos were incubated at 27 ± 1°C on a 14:10 h light/dark cycle. At 24 hours post fertilization (hpf), eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf, overall survival, hatching rates, morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh, aerated test solutions. At 96 hpf again, overall survival, hatching rates, morphological malformations and physiological changes were recorded before RNA and protein extraction. Total RNA and Protein was extracted from the tissue lysate using the NucleoSpin RNA Protein kit (Macherey-Nagel, 740933.250) according to the manufacturer’s protocol. RNA concentration (>100 ng/µl) was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific). The sample’s overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system (Agilent, G2939BA) using the Agilent RNA 6000 Nano Kit© (Agilent, 5067-1511) according to the manufacturer’s protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at -80°C until they were send to the sequencing facility on dry ice. For each sample, 10 4-day old zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples, they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was then carefully removed without injuring the larvae before adding 350µl of RP1 buffer (NucleoSpin RNA Protein kit; Macherey-Nagel 740933.250) for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adapter sequences were removed using trimmomatic (v0.39) and library’s sequence quality was assessed with FastQC (v0.11.5). Reads were checked for potential contaminations with FastQ Screen (v0.14.1) using bowtie2 (v2.3.2) against the following genomes: Daphnia magna (ftp://ftp.ensemblgenomes.org/pub/metazoa/release-48/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz), Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Eschericia coli as well as custom build human rRNA database. With the exception of D. magna, pre-built Bowtie2 indices for those genomes were directly downloaded from Babraham Bioinformatics with the built-in function ‘fastq_screen --get_genomes’.

characteristic: description

text: larval stage

characteristic: developmental stage

text: wild type genotype

text: mixed pool of 10 larvae

characteristic: individual

text: Danio rerio

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: mixed

text: AB


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: ArrayExpress

text: pluripotent stem cell

text: cattle

text: Protocols: PSCs were cultured on maintenance media which was different for each species, including mouse (Mus musculus), marmoset (Callithrix jacchus), rabbit (Oryctolagus cuniculus), human (Homo sapiens), cattle (Bos taurus) and southern white rhinoceros (Ceratotherium simum). RNA was extracted on the day prior to splitting. To differentiate PSCs from different mammalian species into PSM-like cells, PSC cells were directly changed from the maintenance media to the differentiation media. The differentiation protocol consisted on culturing the cells from 2 to 3 days (depending on the species) in CDMi media containing Chiron (CHIR), bFGF, DMH1 and SB-431542. Human and Marmoset cells were first cultured for 24 hours in CDMi media with CHIR, bFGF and Activin A. Mouse cells were first cultured on their maintenance media without IWR-1 for 24 hours. RNA was extracted under the same culturing conditions during the most efficient day of differentiation based on the percentage of cells expressing the PSM marker TBX6. RNA samples were extracted from cultured cells using the RNeasy Mini Kit (cat. no. 74104) following the manufacturer's instructions. On column DNase digestion was performed on all samples. Barcoded stranded mRNA-seq libraries were prepared from 300ng of high quality total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7.

text: wild type genotype

text: Bos taurus

text: Bos taurus

characteristic: replicate

text: Bos taurus


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: induced presomitic mesoderm cell

text: cattle

text: wild type genotype

text: Bos taurus

characteristic: organism

text: Bos taurus

text: pluripotent stem cell

characteristic: progenitor cell type

text: Bos taurus

characteristic: title


text: EMBL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: pluripotent stem cell

text: human

characteristic: common name

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: EMBL

text: public

text: ArrayExpress

text: induced presomitic mesoderm cell

text: human

characteristic: description

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: pluripotent stem cell

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

text: public

text: ArrayExpress

text: pluripotent stem cell

text: white-tufted-ear marmoset

text: wild type genotype

text: Callithrix jacchus

text: Callithrix jacchus

text: Callithrix jacchus


characteristic: External Id

text: EMBL

text: public

text: ArrayExpress

text: induced presomitic mesoderm cell

text: white-tufted-ear marmoset

text: wild type genotype

text: Callithrix jacchus

text: Callithrix jacchus

text: pluripotent stem cell

characteristic: replicate

text: Callithrix jacchus


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: pluripotent stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

characteristic: broker name

text: induced presomitic mesoderm cell

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: pluripotent stem cell

text: Mus musculus


text: EMBL

text: public

text: ArrayExpress

text: pluripotent stem cell

text: rabbit

text: wild type genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

characteristic: title


text: EMBL

characteristic: INSDC last update

text: public

text: ArrayExpress

text: induced presomitic mesoderm cell

text: rabbit

text: wild type genotype

text: Oryctolagus cuniculus

text: Oryctolagus cuniculus

text: pluripotent stem cell

characteristic: progenitor cell type

text: Oryctolagus cuniculus


text: EMBL

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: pluripotent stem cell

text: white rhinoceros

text: wild type genotype

text: Ceratotherium simum

text: Ceratotherium simum

text: Ceratotherium simum


text: EMBL

text: public

characteristic: Submitter Id

text: ArrayExpress

text: induced presomitic mesoderm cell

text: white rhinoceros

characteristic: common name

text: wild type genotype

text: Ceratotherium simum

text: Ceratotherium simum

text: pluripotent stem cell

text: Ceratotherium simum


text: WW0619/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-CHECKLIST

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

text: Department of Endocrinology, Diabetes and Metabolism, University Children's Hospital, University Medical Centre Ljubljana

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Ljubljana 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

text: Severe acute respiratory syndrome coronavirus 2

text: Sequencing of Slovenian WW samples for SARS-CoV-2 variant detection

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: WW0619/22 P-EL

characteristic: Contains RNA extracts (sample codes)

characteristic: Cq (N1)

characteristic: Cq (N2)

characteristic: Date of amplification (ARTIC)

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: INEXTVIR -20

characteristic: Submitter Id

text: Sequenced wastewater sample from Central WWTP Ljubljana 2

characteristic: description

text: wastewater treatment plant influent

text: wastewater treatment plant

text: wastewater treatment plant influent

text: Slovenia

text: virus

characteristic: organism

text: Illumina

characteristic: title

text: wastewater/sludge


text: WW0623/22 P-EL

characteristic: ENA-CHECKLIST

characteristic: Forward file name

text: National Institute of Biology

text: public

characteristic: No. replicate

characteristic: Reverse file name

characteristic: Sequenced where/how

text: INEXTVIR -20

characteristic: Storage location at NIB

text: Sequenced wastewater sample from Central WWTP Koper 1

text: wastewater treatment plant influent

characteristic: environment (biome)

text: wastewater treatment plant

characteristic: environment (feature)

text: wastewater treatment plant influent

characteristic: environment (material)

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: virus

characteristic: investigation type

characteristic: project name

text: Illumina

characteristic: sequencing method

text: wastewater/sludge

characteristic: wastewater/sludge environmental package