characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

text: public

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

characteristic: host age

text: human

text: not provided

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text: not provided

text: Homo sapiens

characteristic: host scientific name

text: male

text: not provided

text: not applicable

text: Oro-Nasopharyngeal swab

characteristic: isolation source host associated

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text: hCoV-19/Ireland/WW-NVRL-S22IRL00370423/2022

characteristic: title

characteristic: virus identifier


status: PUBLIC

tag: attribute

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characteristic: broker name

text: National Virus Reference Laboratory

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text: not provided

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text: Human coronavirus 2019

text: hCov-19 Oxford Nanopore MinION reads obtained following the Artic v3 protocol

text: Ireland

unit: DD

text: Europe / Ireland / Wicklow

unit: years

text: human

characteristic: host common name

text: not provided

text: not provided

characteristic: host health state

text: Homo sapiens

text: female

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text: not provided

characteristic: host subject id

text: not applicable

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text: Oro-Nasopharyngeal swab

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

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text: hCoV-19/Ireland/WW-NVRL-S22IRL00370532/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

text: public

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

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text: human

text: not provided

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text: not provided

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text: female

text: not provided

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characteristic: isolation source host associated

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text: hCoV-19/Ireland/WW-NVRL-S22IRL00361643/2022

characteristic: title

characteristic: virus identifier


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text: National Virus Reference Laboratory

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text: not provided

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text: Ireland

text: Europe / Ireland / Wicklow

text: human

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text: Homo sapiens

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text: Oro-Nasopharyngeal swab

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: NVRL

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characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

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characteristic: common name

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

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text: National Virus Reference Laboratory

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text: Human coronavirus 2019

text: Ireland

text: Europe / Ireland / Wicklow

text: human

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text: not provided

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text: Oro-Nasopharyngeal swab

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text: hCoV-19/Ireland/WW-NVRL-S22IRL00370739/2022


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text: NVRL

text: public

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

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characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

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text: human

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text: male

text: not provided

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characteristic: isolation source host associated

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characteristic: title

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text: National Virus Reference Laboratory

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text: not provided

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text: Human coronavirus 2019

text: Ireland

text: Europe / Ireland / Wicklow

text: human

characteristic: host common name

text: not provided

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text: Homo sapiens

text: male

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text: not provided

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text: not applicable

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text: Oro-Nasopharyngeal swab

characteristic: sample capture status

text: hCoV-19/Ireland/WW-NVRL-S22IRL00370531/2022


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: NVRL

text: public

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

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characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

characteristic: host age

text: human

text: not provided

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text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

text: not provided

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text: Oro-Nasopharyngeal swab

characteristic: isolation source host associated

characteristic: organism

text: hCoV-19/Ireland/WW-NVRL-S22IRL00366969/2022

characteristic: title

characteristic: virus identifier


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text: NVRL

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text: National Virus Reference Laboratory

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text: not provided

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text: Human coronavirus 2019

text: Ireland

text: Europe / Ireland / Wexford

text: human

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text: Homo sapiens

text: male

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text: not provided

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text: not applicable

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text: Oro-Nasopharyngeal swab

characteristic: sample capture status

text: hCoV-19/Ireland/WX-NVRL-S22IRL00361319/2022


characteristic: ENA-CHECKLIST

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text: NVRL

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text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

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characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wexford

characteristic: geographic location (region and locality)

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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: hCoV-19/Ireland/WX-NVRL-S22IRL00361323/2022

characteristic: title

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text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

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text: not provided

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text: Human coronavirus 2019

text: Ireland

text: Europe / Ireland / Wexford

text: human

characteristic: host common name

text: not provided

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text: Homo sapiens

text: male

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text: not provided

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text: not applicable

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text: Oro-Nasopharyngeal swab

characteristic: sample capture status

text: hCoV-19/Ireland/WX-NVRL-S22IRL00361238/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

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text: NVRL

text: public

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text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wexford

characteristic: geographic location (region and locality)

characteristic: host age

text: human

text: not provided

characteristic: host disease outcome

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: male

text: not provided

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text: Oro-Nasopharyngeal swab

characteristic: isolation source host associated

characteristic: organism

text: hCoV-19/Ireland/WX-NVRL-S22IRL00361370/2022

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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text: public

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characteristic: SRA accession

tag: Namespace:Division of Genetics and Genomics, Institute for Molecular Bioscience

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Fresh shaved suspected SCC and BCC lesions and a 4mm punch biopsy of non-sun exposed skin from the same patient were collected in DMEM for immediate tissue dissociation. The tissue sections were rinsed in PBS and incubated in 8 mg/mL Dispase at 37°C for 1h, and were minced before a 3 minutes incubation in 0.25% Trypsin at 37°C. To collect single cells, the suspension was filtered through a 70µm cell strainer. Cells were collected in PBS containing Fetal Calf Serum. Tissue cryosectioned at 10µm thickness were transferred to chilled Visium Tissue Optimization Slides (3000394, 10x Genomics, USA) and Visium Spatial Gene Expression Slides (2000233, 10x Genomics, USA), and allowed to adhere by warming the back of the slide. Tissue sections were dried for one min at 37℃, fixed in chilled 100% methanol for 30 minutes and stained with hematoxylin and eosin for 5 minutes and 2 minutes as per Visium Spatial Tissue Optimization User Guide (CG000238 Rev A, 10x Genomics) or Visium Spatial Gene Expression User Guide (CG000239 Rev A, 10x Genomics) RNA extraction follows 10x protocol for single cell 3' sequencing and Visium FFPE sequencing protocols The 10x Genomics Chromium scRNA-sequencing followed the manufacturer’s instructions, using the Single Cell 3' Library, Gel Bead and Multiplex Kit (version 2, PN-120233; 10x Genomics). Cell numbers in each reaction were optimized to capture approximately 3,000 cells. Visium Spatial Gene Expression library was done following the manufacturer's protocol (CG000239 Rev A, 10x Genomics), using Visium V1, and the barcodes used are (B1:SI-TT-D5; C1: SI-TT-D6; D1: SI-TT-D7).

text: adult

characteristic: developmental stage

text: skin carcinoma

characteristic: disease

text: BCC B18 and SCC E15

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Genetics and Genomics, Institute for Molecular Bioscience

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

text: skin carcinoma

text: SCC F21

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: neoplasm

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

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text: public

text: ArrayExpress

text: human

text: adult

text: skin carcinoma

text: BCC E15 and BCC F21

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: neoplasm

text: Homo sapiens

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

text: adult

characteristic: developmental stage

text: skin carcinoma

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text: Homo sapiens

text: Homo sapiens

text: skin

text: neoplasm

text: Homo sapiens


text: public

text: ArrayExpress

text: human

text: adult

text: skin carcinoma

characteristic: disease

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text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: normal tissue

characteristic: sampling site

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Tartu, Estonia

text: public

text: ena-upload-cli v0.6.0 @ Galaxy

tag: Namespace:University of Tartu, Estonia

characteristic: Submitter Id

text: University of Tartu KoroGenoEST3 consortium, Estonia

characteristic: collecting institution

characteristic: collection date

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

characteristic: collector name

text: Nasopharyngeal/oropharyngeal swab from Estonian Covid-19 patient

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Northern Estonia

characteristic: geographic location (region and locality)

characteristic: host age

text: human

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text: not provided

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text: Homo sapiens

characteristic: host scientific name

text: female

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characteristic: sample capture status

text: PCR tiled amplicon WGS of SARS-Cov-2, pre-selected subset from active surveillance


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

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characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

text: North-Eastern Estonia

text: human

text: not provided

text: Homo sapiens

text: female

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


text: University of Tartu, Estonia

text: public

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Southern Estonia

characteristic: geographic location (region and locality)

characteristic: host age

text: human

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text: not provided

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text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

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text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

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text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: male

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characteristic: host subject id

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text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Central Estonia

text: human

text: not provided

text: Homo sapiens

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characteristic: isolate

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characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: public

characteristic: INSDC status

tag: Namespace:West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: not provided

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

text: not provided

text: not provided

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

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text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Southern Estonia

characteristic: host age

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

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characteristic: isolate

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text: University of Tartu, Estonia

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text: public

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text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

text: Western Estonia

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: female

characteristic: title


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

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text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Western Estonia

characteristic: host age

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

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text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

text: Central Estonia

text: human

text: not provided

text: Homo sapiens

text: male

characteristic: host subject id

characteristic: isolate

characteristic: organism

text: active surveillance not initiated by an outbreak

characteristic: sample capture status

text: PCR tiled amplicon WGS of SARS-Cov-2, monitoring random samples from active surveillance


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Southern Estonia

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

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text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

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text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

characteristic: geographic location (longitude)

text: Western Estonia

characteristic: host age

text: human

text: not provided

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characteristic: host scientific name

text: female

characteristic: host sex


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Northern Estonia

text: human

text: not provided

text: Homo sapiens

text: female

characteristic: host subject id

characteristic: isolate

characteristic: organism

characteristic: sample capture status


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

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text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

text: Southern Estonia

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

characteristic: title


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Central Estonia

characteristic: host age

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: University of Tartu, Estonia

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text: public

characteristic: INSDC status

text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

text: Northern Estonia

text: human

text: not provided

text: Homo sapiens

text: male

characteristic: host subject id

characteristic: isolate

characteristic: organism

characteristic: sample capture status


text: University of Tartu, Estonia

text: public

characteristic: SRA accession

text: ena-upload-cli v0.6.0 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Western Estonia

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Tartu, Estonia

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text: public

characteristic: INSDC status

text: ena-upload-cli v0.6.0 @ Galaxy

text: Estonia

characteristic: geographic location (longitude)

text: Northern Estonia

characteristic: host age

text: human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex


text: Department of Zoology

text: public

characteristic: SRA accession

text: Acrocephalus_arundinaceus_ZA20413_repl.1

tag: Namespace:Department of Zoology

characteristic: Submitter Id

text: House sparrow

characteristic: common name

characteristic: description

text: Passer domesticus

characteristic: organism

text: Passer domesticus

text: Passerine gut microbiota


characteristic: ENA-CHECKLIST

text: Department of Zoology

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text: Acrocephalus_arundinaceus_ZA20413_repl.2

text: House sparrow

text: Passer domesticus

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text: Passerine gut microbiota

characteristic: title


characteristic: ENA-FIRST-PUBLIC

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text: Department of Zoology

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text: Passer domesticus

text: Passer domesticus

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characteristic: External Id

text: Department of Zoology

characteristic: INSDC center name

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text: House sparrow

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text: Passer domesticus

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text: Department of Zoology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Acrocephalus_arundinaceus_ZA21730_repl.2

text: House sparrow

text: Passer domesticus

text: Passer domesticus

text: Passerine gut microbiota


text: Department of Zoology

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characteristic: INSDC status

text: Acrocephalus_arundinaceus_ZA21730_repl.3

text: House sparrow

text: Passer domesticus

text: Passer domesticus

text: Passerine gut microbiota


text: Department of Zoology

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text: House sparrow

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text: Department of Zoology

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text: House sparrow

text: Passer domesticus

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text: Department of Zoology

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text: Acrocephalus_arundinaceus_ZA24402_repl.3

text: House sparrow

text: Passer domesticus

text: Passer domesticus

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text: Department of Zoology

text: public

text: Acrocephalus_arundinaceus_ZA24483_repl.1

text: House sparrow

text: Passer domesticus

text: Passer domesticus

text: Passerine gut microbiota


text: Department of Zoology

text: public

text: Acrocephalus_arundinaceus_ZA24483_repl.2

text: House sparrow

text: Passer domesticus

text: Passer domesticus

text: Passerine gut microbiota


text: Department of Zoology

text: public

text: Acrocephalus_arundinaceus_ZA27389_repl.1

text: House sparrow

text: Passer domesticus

text: Passer domesticus

text: Passerine gut microbiota


text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: public

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

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text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: Department of Zoology

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text: Acrocephalus_arundinaceus_ZA27389_repl.2

characteristic: Submitter Id

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

text: public

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: House sparrow

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text: Department of Zoology

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text: Department of Zoology

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text: House sparrow

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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text: House sparrow

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text: Department of Zoology

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text: Department of Zoology

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text: Department of Zoology

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characteristic: External Id

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tag: Namespace:Anthony Smith, NICD

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