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characteristic: geographic location (longitude)

text: Europe / Ireland / Mayo

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text: Homo sapiens

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text: National Virus Reference Laboratory

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characteristic: virus identifier


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text: Ireland

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characteristic: title


text: NVRL

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text: Human coronavirus 2019

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text: Ireland

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text: Europe / Ireland / Roscommon

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text: NVRL

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text: Europe / Ireland / Roscommon

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text: Ireland

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text: Europe / Ireland / Roscommon

text: human

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characteristic: virus identifier


text: NVRL

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characteristic: title


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text: hCoV-19/Ireland/SO-NVRL-S23IRL00003470/2023


text: NVRL

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text: Europe / Ireland / Sligo

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characteristic: virus identifier


text: NVRL

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characteristic: title


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text: hCoV-19/Ireland/SO-NVRL-S23IRL00002456/2023


text: NVRL

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characteristic: virus identifier


text: NVRL

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text: Europe / Ireland / Sligo

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text: Ireland

characteristic: geographic location (latitude)

text: Europe / Ireland / Sligo

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

characteristic: organism

text: hCoV-19/Ireland/SO-NVRL-S23IRL00002371/2023

characteristic: title


text: NVRL

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text: not provided

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characteristic: geographic location (latitude)

text: Europe / Ireland / Tipperary

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text: Homo sapiens

text: female

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characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

text: hCoV-19/Ireland/TA-NVRL-S22IRL00480051/2022


text: NVRL

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characteristic: collector name

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text: Europe / Ireland / Westmeath

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text: not provided

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text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

text: hCoV-19/Ireland/WH-NVRL-S23IRL00003818/2023

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (latitude)

text: Europe / Ireland / Westmeath

text: human

text: not provided

text: not provided

text: Homo sapiens

text: male

text: not provided

text: Oro-Nasopharyngeal swab

characteristic: organism

text: hCoV-19/Ireland/WH-NVRL-S23IRL00003377/2023

characteristic: virus identifier


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: Europe / Ireland / Westmeath

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: sample capture status

text: hCoV-19/Ireland/WH-NVRL-S23IRL00002315/2023


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (latitude)

text: Europe / Ireland / Wicklow

text: human

text: not provided

text: not provided

text: Homo sapiens

text: male

text: not provided

text: Oro-Nasopharyngeal swab

characteristic: organism

text: hCoV-19/Ireland/WW-NVRL-S23IRL00002393/2023

characteristic: title


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

text: hCoV-19/Ireland/WW-NVRL-S23IRL00002391/2023

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (latitude)

text: Europe / Ireland / Wicklow

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

characteristic: organism

characteristic: sample capture status

text: hCoV-19/Ireland/WW-NVRL-S22IRL00480012/2022


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: Europe / Ireland / Wicklow

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

text: hCoV-19/Ireland/WW-NVRL-S23IRL00002486/2023

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (latitude)

text: Europe / Ireland / Wicklow

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

characteristic: organism

text: hCoV-19/Ireland/WW-NVRL-S23IRL00002485/2023

characteristic: virus identifier


text: public

tag: Namespace:Regional Public Health Authority with the seat in Trenčín, Slovakia

text: Science Park of Comenius University of Bratislava

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: common name

text: Slovakia

characteristic: geographic location (country and/or sea)

characteristic: host age

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: RNA

characteristic: isolate

text: Nasopharyngeal swab

characteristic: isolation source-host associated

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Regional Public Health Authority with the seat in Trenčín, Slovakia

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broker name

text: not provided

text: Slovakia

text: Human

text: not provided

text: Homo sapiens

text: female

text: RNA

text: Nasopharyngeal swab


text: public

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: common name

text: Slovakia

characteristic: geographic location (country and/or sea)

characteristic: host age

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: male

text: RNA

text: Nasopharyngeal swab

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIPH

text: public

text: ELIXIR-Norway

text: S. pyogenes

text: GAS routine sample

characteristic: description

text: Norway

text: not provided

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Bursa

text: Streptococcus pyogenes

text: Streptococcus pyogenes

characteristic: title


text: NIPH

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: S. pyogenes

text: GAS routine sample

text: Norway

text: not provided

text: Homo sapiens

text: Blood

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: NIPH

text: public

text: ELIXIR-Norway

text: S. pyogenes

characteristic: common name

text: GAS routine sample

text: Norway

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

text: abscess

text: Streptococcus pyogenes

text: Streptococcus pyogenes


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NIPH

text: public

text: ELIXIR-Norway

text: S. pyogenes

text: GAS routine sample

text: Norway

text: not provided

text: Homo sapiens

text: otorrhea

text: Streptococcus pyogenes

characteristic: organism

text: Streptococcus pyogenes


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIPH

text: public

text: ELIXIR-Norway

text: S. pyogenes

text: GAS routine sample

characteristic: description

text: Norway

text: not provided

text: Homo sapiens

text: Pleural fluid

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: NIPH

text: public

text: ELIXIR-Norway

text: S. pyogenes

text: GAS routine sample

text: Norway

text: not provided

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Tissue

text: Streptococcus pyogenes

text: Streptococcus pyogenes

characteristic: title


text: EESC/USP

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: non

characteristic: broad-scale environmental context

characteristic: collection date

text: biological reactor

text: biological reactor

characteristic: environmental medium

text: Brazil

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: biological reactor

characteristic: local environmental context

text: metagenome

text: Metatranscriptomic acidogenic reactor

characteristic: project name

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: INSTITUT PASTEUR

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSTITUT PASTEUR

characteristic: Submitter Id

text: France

characteristic: geographic location (country and/or sea)

text: CLIP 2019/00423

text: Food

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes CLIP 2019/00423


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

characteristic: INSDC center name

text: public

text: SIB

characteristic: broker name

text: Spital Langenthal, SRO AG, Labor

characteristic: collecting institution

text: Alexander Imhof, Cedric Howald, Lorenzo Cerutti, Henri Pegeot, Melyssa Elies, Deborah Penet, Keith Harshman, Ioannis Xenarios

characteristic: collector name

text: Switzerland

text: SO

characteristic: geographic location (region and locality)

text: Human

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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/SO-SRO-5000159393/2022

characteristic: isolate

characteristic: sample capture status

text: active surveillance not initiated by an outbreak

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SRO

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: Spital Langenthal, SRO AG, Labor

characteristic: collection date

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-SRO-5000160123/2022

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

characteristic: INSDC center name

text: public

text: SIB

characteristic: broker name

text: Spital Langenthal, SRO AG, Labor

characteristic: collecting institution

characteristic: collector name

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text: Human

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text: restricted access

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text: Homo sapiens

text: restricted access

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text: hCoV-19/Switzerland/BE-SRO-5000158698/2022

text: active surveillance in response to outbreak


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characteristic: host scientific name

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text: hCoV-19/Switzerland/BE-SRO-5000162306/2022

characteristic: isolate

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characteristic: GISAID Accession ID

text: SRO

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text: Spital Langenthal, SRO AG, Labor

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text: Switzerland

characteristic: geographic location (country and/or sea)

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text: Homo sapiens

text: restricted access

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characteristic: organism


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text: restricted access

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text: hCoV-19/Switzerland/BE-SRO-5000159905/2022


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

characteristic: INSDC center name

text: public

text: SIB

text: Spital Langenthal, SRO AG, Labor

text: Switzerland

text: LU

text: Human

text: restricted access

text: Homo sapiens

characteristic: host scientific name

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text: hCoV-19/Switzerland/LU-SRO-5000159349/2022

characteristic: isolate

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text: SRO

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text: SIB

text: Spital Langenthal, SRO AG, Labor

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text: Switzerland

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text: Human

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text: hCoV-19/Switzerland/SO-SRO-2212270087/2022

characteristic: organism


characteristic: ENA-LAST-UPDATE

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text: public

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text: Spital Langenthal, SRO AG, Labor

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characteristic: host scientific name

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characteristic: isolate

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characteristic: External Id

characteristic: GISAID Accession ID

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text: SIB

text: Spital Langenthal, SRO AG, Labor

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text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

text: Human

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text: Homo sapiens

text: restricted access

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text: hCoV-19/Switzerland/BE-SRO-5000162324/2022

characteristic: organism


characteristic: ENA-CHECKLIST

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text: SRO

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text: public

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text: restricted access

text: hCoV-19/Switzerland/BE-SRO-5000161000/2022


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

characteristic: INSDC center name

text: public

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text: restricted access

text: Homo sapiens

characteristic: host scientific name

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text: hCoV-19/Switzerland/BE-SRO-2212210079/2022

characteristic: isolate

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text: Spital Langenthal, SRO AG, Labor

characteristic: collection date

text: Alexander Imhof, Cedric Howald, Lorenzo Cerutti, Henri Pegeot, Melyssa Elies, Deborah Penet, Keith Harshman, Ioannis Xenarios

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

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text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-SRO-5000163841/2022

characteristic: organism


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text: SRO

characteristic: INSDC center name

text: public

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characteristic: collecting institution

characteristic: collector name

text: Switzerland

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characteristic: geographic location (region and locality)

text: Human

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text: hCoV-19/Switzerland/LU-SRO-5000161647/2022

text: active surveillance not initiated by an outbreak


characteristic: ENA-CHECKLIST

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text: hCoV-19/Switzerland/BE-SRO-5000163427/2022

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

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characteristic: GISAID Accession ID

text: SRO

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text: SIB

text: Spital Langenthal, SRO AG, Labor

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text: Switzerland

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text: AG

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text: hCoV-19/Switzerland/AG-SRO-5000165221/2022

characteristic: organism

text: active surveillance in response to outbreak


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text: Human

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text: hCoV-19/Switzerland/BE-SRO-5000163439/2022


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

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text: public

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text: hCoV-19/Switzerland/BE-SRO-5000162961/2022

characteristic: isolate

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text: SRO

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text: Switzerland

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text: Homo sapiens

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text: hCoV-19/Switzerland/BE-SRO-5000162139/2022

characteristic: organism


characteristic: ENA-LAST-UPDATE

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characteristic: GISAID Accession ID

text: SRO

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text: hCoV-19/Switzerland/BE-SRO-5000160913/2022


characteristic: ENA-CHECKLIST

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characteristic: isolate

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text: Human

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text: hCoV-19/Switzerland/SO-SRO-5000163426/2022

characteristic: organism


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text: hCoV-19/Switzerland/BE-SRO-2212270094/2022


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: SRO

characteristic: INSDC center name

text: public

text: SIB

text: Spital Langenthal, SRO AG, Labor

text: Switzerland

text: BE

text: Human

text: restricted access

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-SRO-5000163582/2022

characteristic: isolate

characteristic: sample capture status

characteristic: title


E-MTAB-12593:Sample 1_Cancer

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DUNDEE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12593:Sample 1_Cancer

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The work described in this report is a study using targeted sequencing-based RNA expression analysis on formalin-fixed, paraffin-embedded (FFPE) tissue sections of human prostate. The radical prostatectomy specimens from the 15 male patients included in this study were labelled, weighed and formalin fixed. This included 15 samples from each of three different regions of interest - normal prostate tissue, cancerous tissue, and the microenvironment. An excision of 10mm2 was taken for normal prostate and cancerous regions, and an excision of 5mm2 was taken for microenvironment due to the smaller area available for this region across slides. The radical prostatectomy specimens from the 15 male patients included in this study were labelled, weighed and formalin fixed. Subsequently, the radical prostatectomy specimens were sliced in patient-specific moulds to assist in correlating and adjusting magnetic resonance images with histology. Before an excision of 10mm2 was taken for normal prostate and cancerous regions, and an excision of 5mm2 was taken for microenvironment due to the smaller area available for this region across slides. After the buffers have been prepared, proceed to sample excision. Begin by scraping away paraffin adjacent to the tissue area of interest with a single-edge disposable razor blade. Excess paraffin can form a thick layer on top of the liquid in subsequent steps, inhibiting digestion and mixing. Prepare a new 96-well PCR plate, then proceed with one sample at a time. Add 1.8 μL of 1X Lysis Buffer per mm2 of sample tissue to the well. Attach a fresh sterile tip to a single-channel hand pipet or prepare a sterile plastic toothpick. Use a fresh tip/toothpick for every sample. Excise the target area by scraping it off the glass slide with a disposable razor. Use a fresh razor for each sample. Transfer the excised tissue into the plate well. Use the pipet tip or toothpick to push the sample off the blade, into the well, and down to the bottom of the well. Static electricity may cause the tissue to fly off the transfer tool. This can be prevented by pre-wetting the transfer tool in lysis buffer by dipping it into the well. If using a pipette tip, dispense any liquid that may have entered the tip by capillary action into the well. Overlay sample with molecular biology grade mineral oil. Use 10 μL plus 1 μL per mm2 of tissue in the sample. For example, add 20 μL to a 10 mm2 tissue input. When all samples have been processed, visually inspect the plate to ensure there is tissue at the bottom of each assay well. Spin the plate at 1000 rcf for 2 minutes. Incubate the plate at 95°C for 5 minutes to melt the tissue, then cool it to 4°C for 5 minutes. Add 0.2 μL Protease Mix per mm2 of tissue to the aqueous layer at the bottom of each sample well. For example, add 2 μL for a 10 mm2 input. Mix the aqueous layer by trituration, taking care not to aspirate the tissue sample. Spin the plate at 1000 rcf for 2 minutes to bring the aqueous phase to the bottom of the well. This will also separate the oil/paraffin layer from the lysate. Incubate the plate at 37°C for 30 minutes for tissue lysis. After tissue lysis, visually inspect the wells. You may see tissue fragments in the aqueous layer. To homogenize the lysate, triturate until the lysate becomes uniform. Take care to avoid bubbles. Spin the plate at 1000 rcf for 2 minutes to separate layers. FFPE lysates can be used immediately or stored at -80°C for up to one year. The TempO-Seq assay utilizes a detector oligo (DO) pool specific to the RNA targets to be monitored. BioSpyder offers fixed content and custom DO pools to measure focused sets of transcripts, up to whole transcriptomes. In addition to FFPE tissues, the assay can utilize purified RNA, and cell lysates. Both positive and negative control samples can be included. The TempO-Seq assay does not require extraction or purification of RNA from FFPE samples. Instead, tissue is scraped from a slide into lysis buffer, melted, and lysed. This tissue lysate is directly added into the assay. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of DOs targeting a single transcript. The DO pool targets up to tens of thousands of RNA sequences, depending on the content of the assay. The DOs hybridize to sequences of the targeted RNA molecule such that their respective 3’ and 5’ ends are immediately adjacent. After DO annealing, excess oligos and mis-hybridized or weakly hybridized DOs are removed by nuclease digestion, and the annealed oligos are ligated to form amplifiable templates. The ligated DOs are amplified with one pair of primers (making each PCR reaction single-plex regardless of the number of genes measured). A different combination of sample index/tag sequences can be assigned to each sample. The PCR products are pooled together into a sequencing library, which is then purified and run on an Illumina sequencer to count the number of ligated detector oligo sequences per sample (ThermoFisher-compatible kit under development) . Because TempO-Seq includes an end-point PCR reaction, individual quantitation of the amplified products before library pooling is not needed. Very low concentration and negative control samples are expected to show low reads in the sequencing data. The resulting sequencing read counts from the pooled library can be analyzed to determine the abundance of each gene from each sample. Many types of further analysis are then possible; for example, changes in expression due to treatments or differential expression between samples can be determined. In TempO-Seq, each Detector Oligo consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

characteristic: description

text: prostate cancer

characteristic: disease

text: individual 1

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1_Cancer


E-MTAB-12593:Sample 1_ME

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUNDEE

characteristic: INSDC center name

text: public

text: E-MTAB-12593:Sample 1_ME

text: ArrayExpress

characteristic: broker name

text: human

text: prostate cancer

text: individual 1

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: microenvironment

text: Homo sapiens

text: male

text: Sample 1_ME


E-MTAB-12593:Sample 1_Normal

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DUNDEE

characteristic: INSDC first public

text: public

text: E-MTAB-12593:Sample 1_Normal

text: ArrayExpress

text: human

text: prostate cancer

text: individual 1

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: normal tissue

text: Homo sapiens

text: male

text: Sample 1_Normal

characteristic: title


E-MTAB-12593:Sample 2_Cancer

text: DUNDEE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12593:Sample 2_Cancer

characteristic: Submitter Id

text: ArrayExpress

text: human

text: prostate cancer

text: individual 2

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: neoplasm

text: Homo sapiens

text: male

text: Sample 2_Cancer


E-MTAB-12593:Sample 2_ME

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 2_ME

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: prostate cancer

characteristic: disease

text: individual 2

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: microenvironment

text: Homo sapiens

text: male

text: Sample 2_ME


E-MTAB-12593:Sample 2_Normal

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 2_Normal

text: ArrayExpress

text: human

text: prostate cancer

text: individual 2

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: normal tissue

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: Sample 2_Normal


E-MTAB-12593:Sample 3_Cancer

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUNDEE

characteristic: INSDC center name

text: public

text: E-MTAB-12593:Sample 3_Cancer

text: ArrayExpress

characteristic: broker name

text: human

text: prostate cancer

text: individual 3

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: neoplasm

text: Homo sapiens

text: male

text: Sample 3_Cancer


E-MTAB-12593:Sample 3_ME

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DUNDEE

characteristic: INSDC first public

text: public

text: E-MTAB-12593:Sample 3_ME

text: ArrayExpress

text: human

text: prostate cancer

text: individual 3

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: microenvironment

text: Homo sapiens

text: male

text: Sample 3_ME

characteristic: title


E-MTAB-12593:Sample 3_Normal

text: DUNDEE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12593:Sample 3_Normal

characteristic: Submitter Id

text: ArrayExpress

text: human

text: prostate cancer

text: individual 3

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: normal tissue

text: Homo sapiens

text: male

text: Sample 3_Normal


E-MTAB-12593:Sample 4_Cancer

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 4_Cancer

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: prostate cancer

characteristic: disease

text: individual 4

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: neoplasm

text: Homo sapiens

text: male

text: Sample 4_Cancer


E-MTAB-12593:Sample 4_ME

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 4_ME

text: ArrayExpress

text: human

text: prostate cancer

text: individual 4

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: microenvironment

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: Sample 4_ME


E-MTAB-12593:Sample 4_Normal

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUNDEE

characteristic: INSDC center name

text: public

text: E-MTAB-12593:Sample 4_Normal

text: ArrayExpress

characteristic: broker name

text: human

text: prostate cancer

text: individual 4

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: normal tissue

text: Homo sapiens

text: male

text: Sample 4_Normal


E-MTAB-12593:Sample 5_Cancer

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DUNDEE

characteristic: INSDC first public

text: public

text: E-MTAB-12593:Sample 5_Cancer

text: ArrayExpress

text: human

text: prostate cancer

text: individual 5

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: neoplasm

text: Homo sapiens

text: male

text: Sample 5_Cancer

characteristic: title


E-MTAB-12593:Sample 5_ME

text: DUNDEE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12593:Sample 5_ME

characteristic: Submitter Id

text: ArrayExpress

text: human

text: prostate cancer

text: individual 5

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: microenvironment

text: Homo sapiens

text: male

text: Sample 5_ME


E-MTAB-12593:Sample 5_Normal

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 5_Normal

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: prostate cancer

characteristic: disease

text: individual 5

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: normal tissue

text: Homo sapiens

text: male

text: Sample 5_Normal


E-MTAB-12593:Sample 6_Cancer

text: DUNDEE

text: public

text: E-MTAB-12593:Sample 6_Cancer

text: ArrayExpress

text: human

text: prostate cancer

text: individual 6

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: prostate gland

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: Sample 6_Cancer


E-MTAB-12593:Sample 6_ME

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DUNDEE

characteristic: INSDC center name

text: public

text: E-MTAB-12593:Sample 6_ME

text: ArrayExpress

characteristic: broker name

text: human

text: prostate cancer

text: individual 6

text: Homo sapiens

text: Homo sapiens

text: prostate gland

text: microenvironment

text: Homo sapiens

text: male

text: Sample 6_ME