characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: General Hospital of Halkidiki

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA


status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:INSTITUTE OF APPLIED BIOSCIENCES - CERTH

characteristic: Submitter Id

text: General Hospital of Halkidiki

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Chalkidiki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSTITUTE OF APPLIED BIOSCIENCES - CERTH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: General Hospital of Halkidiki

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Chalkidiki

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: General Hospital of Serres

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Serres

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: General Hospital of Serres

text: not provided

text: Greece

text: Serres

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: General Hospital of Katerini

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Katerini

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: General Hospital of Katerini

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Katerini

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece

text: not provided

text: Greece

text: Katerini

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Alexandroupoli

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Giannitsa

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: Greece

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: University General Hospital of Thessaloniki, AHEPA

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Katerini

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Thessaloniki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: not provided

text: Greece

text: Kozani

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Kilkis

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: Greece

text: Serres

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Chalkidiki

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Chalkidiki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Laboratory of Molecular Biology, Mamatsio General Hospital of Kozani

text: not provided

text: Greece

text: Ptolemaida

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Grevena

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Kozani

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: Greece

text: Kastoria

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Veroia

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Edessa

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: not provided

text: Greece

text: Giannitsa

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: General Hospital of Kavala

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Kavala

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: General Hospital of Kavala

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Kavala

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: General Hospital of Goumenissa

text: not provided

text: Greece

text: Kilkis

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: General Hospital of Goumenissa

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Kilkis

text: human

text: not provided

text: Homo sapiens

text: female

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: General Hospital of Drama

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Drama

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: General Hospital of Drama

text: not provided

text: Greece

text: Serres

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Theageneio Hospital of Thessaloniki

text: not provided

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: Papageorgiou, general hospital of Thessaloniki

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

text: Greece

text: Thessaloniki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: not provided

text: Greece

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

characteristic: organism

characteristic: sample capture status

characteristic: title


E-MTAB-11242:CTRL 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Gustave Roussy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11242:CTRL 1

tag: Namespace:Gustave Roussy

text: 7 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Tumor Cell Line: RET melanoma cell line, generated by transgenic expression of the Ret protooncogene under the control of the metallothionein-1 promoter driving spontaneous melanogenesis, was provided by Viktor Umansky (DKFZ ��� German Cancer Research Center; syngeneic from C57BL/6J mice). Mice: All animal experiments were carried out in compliance with French and European laws and regulations. The local institutional animal ethics board and French Research Ministery of approved all mouse experiments (permission numbers: 2020_035_25416). Experiments were performed in accordance with government and institutional guidelines and regulations. Female C57BL/6 were purchased from Harlan (France). Mice were used between 7 and 12 weeks of age. All mouse experiments were performed at the animal facility of Gustave Roussy Cancer Campus where animals were housed in specific pathogen-free conditions. Three mice were implanted with 0.5x10^6 RET melanoma cells subcutaneously. Single-cell Sample Process: Ileum samples from C57BL/6 mice with and without RET melanoma were collected and fat tissue, Peyer���s patches and feces were removed. Intestines were cut longitudinally, rolled up and then cut transversally into small pieces into a tube. Pieces were transferred into a new 50-ml tube with 20 ml of intestinal epithelial cells (IEC) medium containing PBS, 5% FCS, 5 mM EDTA and 1 mM DTT. Tubes were vortexed and shaken at 37 ��C for 20 min. Cell suspensions were filtered with a 40 ��m cell strainer into a new tube, centrifuged, resuspended in a solution of PBS 1X (without EDTA and magnesium) containing 0.04% de BSA (400 ��g/ml) and counted. Cell suspensions were stored in LoBind tubes at a concentration of 1.0 x 10 6 cellules/mL and kept on ice until use. Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer���s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer���s instructions. The resulting libraries were prepared in parallel in one single batch. We pooled all of the libraries for sequencing in an Illumina flow cell. All the libraries were sequenced with an 8-base index read, a 28-base Read1 containing cell-identifying barcodes and unique molecular identifiers (UMIs), and a 91-base Read2 containing transcript sequences on an Illumina NovaSeq 6000 at Gustave Roussy. Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer���s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer���s instructions. The resulting libraries were prepared in parallel in one single batch.

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: ileum

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: CTRL 1

characteristic: xenograft


E-MTAB-11242:CTRL 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Gustave Roussy

text: public

text: E-MTAB-11242:CTRL 2

characteristic: Submitter Id

text: 7 to 12

text: ArrayExpress

text: house mouse

characteristic: common name

text: adult

text: wild type genotype

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: ileum

text: Mus musculus

text: female

text: CTRL 2

characteristic: title


E-MTAB-11242:CTRL 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Gustave Roussy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11242:CTRL 3

text: 7 to 12

text: ArrayExpress

text: house mouse

text: adult

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: ileum

text: Mus musculus

text: female

text: CTRL 3


E-MTAB-11242:RET 1

text: Gustave Roussy

text: public

text: E-MTAB-11242:RET 1

text: 7 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: ileum

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: RET 1

text: 0.5x10^6 RET melanoma cells subcutaneously until neoplasm


E-MTAB-11242:RET 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Gustave Roussy

text: public

text: E-MTAB-11242:RET 2

characteristic: Submitter Id

text: 7 to 12

text: ArrayExpress

text: house mouse

characteristic: common name

text: adult

text: wild type genotype

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: ileum

text: Mus musculus

text: female

characteristic: strain

text: RET 2

characteristic: xenograft


E-MTAB-11242:RET 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Gustave Roussy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11242:RET 3

text: 7 to 12

text: ArrayExpress

text: house mouse

text: adult

text: wild type genotype

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: ileum

text: Mus musculus

text: female

text: RET 3

characteristic: title


text: UNIVERSITY OF QUEENSLAND

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF QUEENSLAND

text: BW25113-chloramphenicol library exposed to sub-inhibitory concentration of polymyxin B

characteristic: description

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

characteristic: GISAID Accession ID

text: public

tag: Namespace:Institute for Infectious Diseases, Bern, Switzerland

text: SIB

characteristic: broker name

text: Inselspital Bern (Covid-Track); Bern, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Nicole Liechti, Christian Baumann, Miguel A Terrazos Miani, Sonja Gempeler, Loïc Borcard, Stefan Neuenschwander, Cora Sägesser, Pascal Bittel, Peter Keller, Franziska Suter-Riniker, Stephen L Leib, Alban Ramette

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BE-IFIK-4902-5598/2021

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Infectious Diseases, Bern, Switzerland

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: SIB

text: Inselspital Bern; Bern, Switzerland

text: Switzerland

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-4903-4679/2021

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

text: SIB

characteristic: broker name

text: Spital Nidwalden, Labor, Stans, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: NW

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/NW-IFIK-4904-1460/2021


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: Switzerland

text: NW

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/NW-IFIK-4905-1461/2021

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Switzerland

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-4906-1745/2021

characteristic: isolate

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

text: public

tag: Namespace:INSTITUT PASTEUR

text: Paenibacillus sp. JJ-60

text: Paenibacillus sp. JJ-60

text: whole genome sequencing of Paenibacillus sp. JJ-60 = CIP111894


characteristic: INSDC first public

text: public

text: SIB

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

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text: Nicole Liechti, Christian Baumann, Miguel A Terrazos Miani, Sonja Gempeler, Loïc Borcard, Stefan Neuenschwander, Cora Sägesser, Pascal Bittel, Peter Keller, Franziska Suter-Riniker, Stephen L Leib, Alban Ramette

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text: JVA Thorberg; Krauchthal, Switzerland

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text: hCoV-19/Switzerland/BE-IFIK-4860-4385/2021

characteristic: organism

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text: public

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text: Inselspital Bern; Bern, Switzerland

text: Switzerland

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text: hCoV-19/Switzerland/BE-IFIK-211206_os_62/2021


characteristic: ENA-FIRST-PUBLIC

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text: public

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tag: Namespace:Center for Laboratory Medicine St. Gallen

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text: Center for Laboratory Medicine, St. Gallen, Switzerland

text: Yannick Gerth

text: Switzerland

text: SG

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text: restricted access

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text: restricted access

text: restricted access

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text: hCoV-19/Switzerland/SG-CLM-12114562/2021

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text: public

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text: Lighthouse Lab in Milton Keynes

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Lighthouse Lab in Milton Keynes by The Lighthouse Lab in Milton Keynes and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

characteristic: description

text: United Kingdom

text: England

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

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text: Lighthouse Lab in Milton Keynes

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Wales

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text: Human

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text: not provided

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text: not provided

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text: not provided

text: not provided


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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Lighthouse Lab in Glasgow

text: not provided

text: Samples prepared at Lighthouse Lab in Glasgow by Harper VanSteenhouse, Yumi Kasai, David Gray, Carol Clugston, Anna Dominiczak and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

text: England

text: Human

text: not provided

text: Human

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

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characteristic: External Id

text: SC

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text: public

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text: Lighthouse Lab in Glasgow

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: description

text: United Kingdom

text: Scotland

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SC

text: Lighthouse Lab in Alderley Park

text: not provided

text: Samples prepared at Lighthouse Lab in Alderley Park by Jacquelyn Wynn, Mairead Hyland, The Lighthouse Lab in Alderley Park and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SC

characteristic: broker name

text: not provided

text: Samples prepared at Berkshire and Surrey Pathology Services Lighthouse Laboratory by Berkshire and Surrey Pathology Services Lighthouse Laboratory and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team

text: United Kingdom

text: England

text: Human

text: not provided

text: Human

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

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text: public

characteristic: INSDC status

text: SC

text: Lighthouse Lab in Alderley Park

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: description

text: United Kingdom

text: Wales

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC

text: not provided

text: Samples prepared at Virology Department, Royal Infirmary of Edinburgh, NHS Lothian / School of Biological Sciences, University of Edinburgh by McHugh M, Dewar R, Rooke S, O'Toole Á, Scher E, Hill V, McCrone JT, Colquhoun R, Yu X, Jackson B, Rambaut A, Templeton K and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

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text: Human

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text: not provided

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text: not provided

text: not provided


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

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text: SC

characteristic: broker name

text: Virology Department, Royal Infirmary of Edinburgh, NHS Lothian / School of Biological Sciences, University of Edinburgh

text: not provided

text: United Kingdom

text: Scotland

text: Human

text: not provided

text: Human

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: Animal and Plant Health Agency

characteristic: INSDC center name

text: public

tag: Namespace:Animal and Plant Health Agency

characteristic: collection date

text: Isolated from Tortoise

characteristic: description

text: United Kingdom

text: diseased

text: Centrochelys sulcata

text: lung tissue

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

text: Isolation of a blaCTX-M-15-associated Klebsiella pneumoniae ST307 in a tortoise in the UK.

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text: GSC

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text: public

text: Aegilops ventricosa

text: Aegilops ventricosa


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:CIBIO RESEARCH CENTER IN BIODIVERSITY AND GENETIC RESOURCES

characteristic: common name

text: bottled water 100ml

text: No

text: A

text: Italy

characteristic: geographic location (country and/or sea)

text: Maggiore

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text: public

characteristic: SRA accession

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text: lake

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text: Maggiore

text: 45.93321 N 8.484536 E

text: freshwater metagenome

text: water

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characteristic: ENA-FIRST-PUBLIC

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text: lake

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text: A

text: Italy

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text: 45.843542 N 8.573045 E

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text: 45.703603 N 8.649786 E

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text: 45.975686 N 8.847133 E

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text: Varese

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text: 45.819905 N 8.715954 E

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text: 45.795364 N 8.756557 E

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text: lake

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text: Yes

text: A

text: Portugal

text: Caniçada

text: 41.6518846 N -8.2277663 E

text: freshwater metagenome

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text: freshwater metagenome


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text: lake

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text: 41.6512575 N -8.2154335 E

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text: 41.6768212 N -8.182258 E

text: freshwater metagenome

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text: bottled water 100ml

text: No

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text: Portugal

text: Castelo de Bode

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text: 39.544663 N -8.304957 E

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text: public

text: PCRNC

text: No

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text: metagenome


text: public

text: No

text: A

text: metagenome

text: metagenome


text: SC

text: public

text: SC

characteristic: broker name

text: Lighthouse Lab in Glasgow

characteristic: collecting institution

characteristic: collection date

text: not provided

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text: United Kingdom

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text: United Kingdom

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text: not provided

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text: not provided

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text: Scotland

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text: not provided

text: not provided

text: not provided


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text: not provided

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text: public

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text: SC

text: Lighthouse Lab in Alderley Park

text: not provided

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Integrated Covid Hub North East

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Integrated Covid Hub North East by Integrated Covid Hub North East and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team

text: United Kingdom

text: England

text: Human

characteristic: host common name

text: not provided

text: Human

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC

text: Lighthouse Lab in Alderley Park

text: not provided

text: United Kingdom

text: Wales

text: Human

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SC

text: Berkshire and Surrey Pathology Services Lighthouse Laboratory

text: not provided

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Rosalind Franklin Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Rosalind Franklin Laboratory by Donald Fraser, Suki Lee, Rob Howes, The Rosalind Franklin Laboratory and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team

text: United Kingdom

text: England

text: Human

characteristic: host common name

text: not provided

text: Human

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

text: SC

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characteristic: INSDC last update

text: public

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text: SC

text: Rosalind Franklin Laboratory

text: not provided

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text: Wales

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text: Human

characteristic: host scientific name

text: not provided

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text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: SC

text: Lighthouse Lab in Milton Keynes

text: not provided

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Wales

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Lighthouse Lab in Milton Keynes

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: United Kingdom

text: Scotland

text: Human

characteristic: host common name

text: not provided

text: Human

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC

text: Lighthouse Laboratory Plymouth

text: not provided

text: Samples prepared at Lighthouse Laboratory Plymouth by Lighthouse Laboratory Plymouth and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

text: England

text: Human

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

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characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

text: SC

text: Lighthouse Lab in Alderley Park

text: not provided

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:175-126

tag: Namespace:NCYC - National Collection of Yeast Cultures

characteristic: Submitter Id

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 140


text: NCYC - National Collection of Yeast Cultures

text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:176-127

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 4020


text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:176-128

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 161


text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:177-129

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 3506


text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:177-130

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 2629


text: public

text: ena-SAMPLE-TAB-17-12-2021-10:43:06:177-131

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 3877


text: public

text: ena-SAMPLE-TAB-17-12-2021-10:54:55:761-134

text: Torulaspora delbrueckii

text: Torulaspora delbrueckii

text: NCYC 3024


characteristic: GISAID Accession ID

text: Center for Laboratory Medicine St. Gallen

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text: Center for Laboratory Medicine, St. Gallen, Switzerland

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text: Yannick Gerth

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text: Homo sapiens

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characteristic: geographic location (region and locality)

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

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text: hCoV-19/Switzerland/SG-CLM-11178165/2021

text: Severe acute respiratory syndrome coronavirus 2

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text: Yannick Gerth

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characteristic: organism

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text: Yannick Gerth

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characteristic: ENA-FIRST-PUBLIC

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characteristic: ENA-FIRST-PUBLIC

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text: Protocols: Samples were collected using the Qiagen RNeasy kit following manufacturers instructions. Qiagen RNeasy kit was used to extract total RNA from cells. Twenty-seven total RNA samples were processed using the Illumina Stranded Total RNA w/Ribo-Zero Plus assay. One-hundred nanograms of each total RNA sample (quantitated on the Invitrogen Qubit 2.0 Fluorometer using the Qubit RNA HS Assay Kit) was subjected to ribosomal RNA (rRNA) depletion through an enzymatic process, which includes reduction of human mitochondrial and cytoplasmic rRNAs. Following rRNA depletion and purification, RNA was primed with random hexamers for first-strand cDNA synthesis, then second-strand cDNA synthesis. During second-strand cDNA synthesis, deoxyuridine triphosphate (dUTP) was incorporated in place of deoxythymidine triphosphate (dTTP) to achieve strand specificity in a subsequent amplification step. Next, adenine (A) nucleotide was added to the 3’ ends of the blunt fragments to prevent ends from ligating to each other. The A-tail also provides a complementary overhang to the thymine (T) nucleotide on the 3’ end of the adapter. During adapter ligation and amplification, indexes and adapters were added to both ends of the fragments, resulting in 10bp, dual-indexed libraries, ready for cluster generation and sequencing. The second-strand was quenched during amplification due to the incorporation of dUTP during second-strand cDNA synthesis, allowing for only the antisense strand to be sequenced in Read 1. Thirteen cycles of amplification were performed.

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text: SARS-CoV-2 isolate VIC

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text: University of Tartu, Estonia

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text: ena-upload-cli v0.4.3 @ Galaxy

tag: Namespace:University of Tartu, Estonia

text: University of Tartu KoroGenoEST3 consortium, Estonia

characteristic: collecting institution

text: Aare Abroi, Radko Avi, Taavi Päll, Heiki Niglas , Merit Pauskar, Arina Shablinskaja, Eveli Kallas, Andrio Lahesaare, Kai Truusalu, Dagmar Hoidmets, Olga Sadikova, Kaspar Ratnik, Hanna Sepp, Liidia Dotsenko, Jevgenia Epštein, Heleene Suija, Katrin Kaarna, Lili Milani, Mait Metspalu, Ott Eric Oopkaup, Ivar Koppel, Erik Jaaniso, Ivan Kuzmin, Uku Raudvere, Tuuli Reisberg, Hedi Peterson, Ulvi Gerst Talas, Paul Naaber, Mari-Anne Härma, Irja Lutsar, Kristi Huik

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text: University of Tartu, Estonia

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text: University of Tartu, Estonia

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text: Nicole Liechti, Christian Baumann, Miguel A Terrazos Miani, Sonja Gempeler, Loïc Borcard, Stefan Neuenschwander, Cora Sägesser, Pascal Bittel, Peter Keller, Franziska Suter-Riniker, Stephen L Leib, Alban Ramette

text: Switzerland

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text: hCoV-19/Switzerland/BE-IFIK-5048-9068/2021

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