characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Natural History Museum

characteristic: GAL

text: Tree of Life Programme

text: public

characteristic: Submitter Id

text: RYAN MITCHELL

text: Oxford University Museum of Natural History

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Oxfordshire | Hartslock Reserve

text: Woodland, grassland, hedges

text: RYAN MITCHELL

text: not collected

text: Spiroplasma endosymbiont of Thecophora atra

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oxford

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Tree of Life Programme

text: Douglas Boyes

text: University of Oxford

unit: m

characteristic: elevation

text: United Kingdom

unit: DD

text: Berkshire | Wytham woods

characteristic: geographic location (region and locality)

text: Woodland

characteristic: habitat

text: Douglas Boyes

text: University of Oxford

text: not collected

characteristic: lifestage

text: Spiroplasma endosymbiont of Monopis laevigella

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: Y


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Natural History Museum

characteristic: GAL

text: Tree of Life Programme

text: public

characteristic: Submitter Id

text: GAVIN BROAD | CHRIS FLETCHER | INEZ JANUSZCZAK

text: Natural History Museum | NATURAL HISTORY MUSEUM | NATURAL HISTORY MUSEUM

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: England | Wytham Woods, Bert's Pheasant Pen

text: NOT COLLECTED

text: GAVIN BROAD

text: Natural History Museum

text: not collected

text: Spiroplasma endosymbiont of Diplazon laetatorius

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT APPLICABLE

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Oxford

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Liam Crowley | James McCulloch

text: University of Oxford | University of Oxford

characteristic: elevation

text: United Kingdom

text: Berkshire | Wytham Woods

characteristic: geographic location (region and locality)

text: Woodland

characteristic: habitat

text: Liam Crowley

text: University of Oxford

text: not collected

characteristic: lifestage

text: Spiroplasma endosymbiont of Cantharis nigra

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT APPLICABLE

text: Y


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: Tree of Life Programme

text: public

characteristic: Submitter Id

text: LIAM CROWLEY

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Wytham Great Wood

text: Woodland

text: LIAM CROWLEY

text: University of Oxford

text: not collected

text: Candidatus Mesenet endosymbiont of Phosphuga atrata

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: Y


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Sanger Institute

text: K7 11

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ANDRES DE LA FILIA

text: University of Edinburgh

text: United Kingdom

text: not provided

text: not provided

characteristic: geographic location (longitude)

text: Lab culture

text: NOT PROVIDED

text: LAURA ROSS

text: University of Edinburgh

text: not collected

text: Candidatus Moranella endobia

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: Candidatus Moranella endobia

text: NOT COLLECTED

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Natural History Museum

characteristic: GAL

text: Tree of Life Programme

text: public

characteristic: Submitter Id

text: ANDREW FARR

text: Riverfly Recording Scheme

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Powdermill Reservoir

characteristic: geographic location (region and locality)

text: NOT PROVIDED

characteristic: habitat

text: ANDREW FARR

text: Riverfly Recording Scheme

text: not collected

characteristic: lifestage

text: Rickettsia endosymbiont of Sialis lutaria

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT APPLICABLE

text: Y


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Natural History Museum

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ENVIRONMENT AGENCY

text: Environment Agency

text: United Kingdom

characteristic: geographic location (latitude)

text: Gloucester Sharpness Canal

text: Freshwater

text: ENVIRONMENT AGENCY

text: Environment Agency

text: not collected

text: Rickettsia endosymbiont of Piscicola geometra

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: Y


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: RO MG 799

text: Tree of Life Programme

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: KONRAD LOHSE | ALEX HAYWARD | DOMINIK LAETSCH | ROGER VILA

text: University of Edinburgh | University of Edinburgh | University of Edinburgh | University of Edinburgh

characteristic: collecting institution

characteristic: collection date

text: Romania

characteristic: geographic location (longitude)

text: NOT PROVIDED

text: NOT PROVIDED

text: ROGER VILA

text: University of Edinburgh

text: not collected

text: Spiroplasma endosymbiont of Melanargia galathea

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Sanger Institute

text: BU CC 715

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SAM EBDON | ALEX MACINTOSH

text: University of Edinburgh | University of Edinburgh

text: Spain

characteristic: geographic location (country and/or sea)

text: Aragon | Bujaruelo

characteristic: geographic location (region and locality)

text: NOT PROVIDED

characteristic: habitat

text: KONRAD LOHSE

text: University of Edinburgh

text: not collected

characteristic: lifestage

text: Spiroplasma endosymbiont of Colias croceus

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT PROVIDED

text: Y


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Anthony Smith, NICD

text: public

characteristic: SRA accession

tag: Namespace:Anthony Smith, NICD

characteristic: Submitter Id

text: EnteroBase

characteristic: broker name

text: EnteroBase

text: A. Smith, National Institute for Communicable Diseases

text: Whole genome sequencing data uploaded by EnteroBase user

characteristic: description

text: South Africa

text: Gauteng

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis

characteristic: serovar

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Anthony Smith, NICD

characteristic: INSDC center name

text: public

text: EnteroBase

text: EnteroBase

characteristic: collection date

text: South Africa

text: Gauteng

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Anatum

characteristic: title


text: Anthony Smith, NICD

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: EnteroBase

text: EnteroBase

text: South Africa

characteristic: geographic location (country and/or sea)

text: Gauteng

characteristic: geographic location (region and locality)

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Anthony Smith, NICD

text: public

text: EnteroBase

text: EnteroBase

text: South Africa

text: Gauteng

text: Human, Other

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Infantis


text: Anthony Smith, NICD

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: EnteroBase

characteristic: broker name

text: EnteroBase

text: South Africa

text: Western Cape

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Heidelberg


text: Anthony Smith, NICD

text: public

text: EnteroBase

text: EnteroBase

characteristic: description

text: South Africa

text: KwaZulu-Natal

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Dublin

characteristic: serovar

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Anthony Smith, NICD

characteristic: INSDC center name

text: public

text: EnteroBase

text: EnteroBase

text: South Africa

text: Gauteng

text: Human, Stool

text: Salmonella enterica

text: Salmonella enterica

text: Give


text: Sanger Institute

characteristic: GAL

text: RO MG 799

text: Tree of Life Programme

characteristic: INSDC first public

text: public

characteristic: collecting institution

characteristic: collection date

text: Romania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: NOT PROVIDED

text: NOT PROVIDED

characteristic: habitat

text: ROGER VILA

text: University of Edinburgh

text: not collected

characteristic: lifestage

text: Wolbachia endosymbiont (group B) of Melanargia galathea

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: K1 2

text: Tree of Life Programme

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: LAURA ROSS

text: University of Edinburgh

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: London | South Kensington | Atherstone Mews

characteristic: geographic location (region and locality)

text: NOT PROVIDED

text: GILLAN WATSON

text: Natural History Museum

text: not collected

text: Candidatus Walczuchella endosymbiont of Icerya purchasi

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT PROVIDED

text: Y


text: Sanger Institute

characteristic: GAL

text: K4-1 2

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: LAURA ROSS

text: University of Edinburgh

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: London | Soth Kensington | Queens gate

text: NOT PROVIDED

characteristic: habitat

text: GILLAN WATSON

text: Natural History Museum

text: not collected

characteristic: lifestage

text: secondary endosymbiont of Balanococcus diminutus

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

text: NOT COLLECTED

text: NOT PROVIDED

text: Y


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: K7 3

text: Tree of Life Programme

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ANDRES DE LA FILIA

text: University of Edinburgh

text: United Kingdom

text: not provided

text: not provided

text: Scotland | Edinburgh Botanical Garden | Lab culture

text: NOT PROVIDED

text: LAURA ROSS

text: University of Edinburgh

text: not collected

text: secondary endosymbiont of Pseudococcus viburni

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ANDREW LUCAS

text: NATURAL RESOURCE WALES

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Cwm Clydach

characteristic: geographic location (region and locality)

text: Oak Woodland

text: ANDREW LUCAS

text: NATURAL RESOURCE WALES

text: not collected

text: Rickettsiales endosymbiont of Leucozona glaucia

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT APPLICABLE

text: Y


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Natural History Museum

text: Tree of Life Programme

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ANDREW FARR

text: Riverfly Recording Scheme

text: United Kingdom

characteristic: geographic location (longitude)

text: Yorkshire | River Rye

text: NOT PROVIDED

characteristic: habitat

text: ANDREW FARR

text: Riverfly Recording Scheme

text: not collected

characteristic: lifestage

text: Rickettsiales endosymbiont of Ecdyonurus torrentis

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

text: NOT COLLECTED

text: NOT APPLICABLE

text: Y


text: Sanger Institute

characteristic: GAL

text: K4-1 2

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: LAURA ROSS

text: University of Edinburgh

characteristic: collecting institution

text: United Kingdom

text: London | Soth Kensington | Queens gate

text: NOT PROVIDED

text: GILLAN WATSON

text: Natural History Museum

text: not collected

text: Candidatus Tremblaya endosymbiont of Balanococcus diminutus

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

characteristic: sample symbiont of

text: NOT COLLECTED

characteristic: sex

text: NOT PROVIDED

text: Y

characteristic: symbiont

characteristic: title

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: K7 3

text: Tree of Life Programme

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ANDRES DE LA FILIA

text: University of Edinburgh

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (region and locality)

text: NOT PROVIDED

text: LAURA ROSS

text: University of Edinburgh

text: not collected

text: Candidatus Tremblaya endosymbiont of Pseudococcus viburni

characteristic: organism

text: **OTHER SOMATIC ANIMAL TISSUE**

text: dtol

text: NOT COLLECTED

text: NOT PROVIDED

text: Y


text: Sanger Institute

characteristic: GAL

text: K7 11

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ANDRES DE LA FILIA

text: University of Edinburgh

characteristic: collecting institution

text: United Kingdom

text: not provided

text: not provided

characteristic: geographic location (longitude)

text: Lab culture

text: NOT PROVIDED

characteristic: habitat

text: LAURA ROSS

text: University of Edinburgh

text: not collected

characteristic: lifestage

text: Candidatus Tremblaya endosymbiont of Planococcus citri

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: dtol

characteristic: project name

text: NOT COLLECTED

text: NOT PROVIDED

text: Y


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Laboratory of Molecular Infection Medicine Sweden (MIMS), Umeå university

text: ArrayExpress

characteristic: broker name

text: lung fibroblast

text: not collected

text: human

characteristic: common name

text: Protocols: HBECs were grown and differentiated at an air-liquid interface (ALI) forming an in vitro 3D-lung model. In short, HBECs were grown and differentiated on 6.5 mm semipermeable transwell inserts (0.4 µm Pore Polyester Membrane Insert, Corning) and after two weeks at air-liquid interface (ALI) the cultures reached full differentiation, which was assessed using light microscopy focusing on epithelial morphology, presence of ciliated cells, and mucus production along with immunofluorescence staining for ciliated cells (acetylated-tubulin, T6793, Sigma) and goblet cells (muc5AC, Ab-1 (45M1), #MS-145-P, ThermoFisher). Primary human bronchial epithelial cells (HBEC) were isolated from proximal airway tissue obtained with informed consent from a patient. At 96 h post infection the mock treated, infected and infected +betamethasone treated HBEC ALI-cultures were washed three times on both sides with PBS. The HBEC ALI-cultures were then lysed and RNA extraction was done using the NucleoSpin RNA II kit (Macherey-Nagel) following the manufacturer’s instructions. RNA-seq libraries were prepared using the Smart-seq2 method

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: mock

characteristic: infect

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

characteristic: title

characteristic: umuwell


text: Laboratory of Molecular Infection Medicine Sweden (MIMS), Umeå university

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: lung fibroblast

text: not collected

characteristic: collection date

text: human

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: mock

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: lung fibroblast

text: not collected

text: human

text: Protocols: HBECs were grown and differentiated at an air-liquid interface (ALI) forming an in vitro 3D-lung model. In short, HBECs were grown and differentiated on 6.5 mm semipermeable transwell inserts (0.4 µm Pore Polyester Membrane Insert, Corning) and after two weeks at air-liquid interface (ALI) the cultures reached full differentiation, which was assessed using light microscopy focusing on epithelial morphology, presence of ciliated cells, and mucus production along with immunofluorescence staining for ciliated cells (acetylated-tubulin, T6793, Sigma) and goblet cells (muc5AC, Ab-1 (45M1), #MS-145-P, ThermoFisher). Primary human bronchial epithelial cells (HBEC) were isolated from proximal airway tissue obtained with informed consent from a patient. At 96 h post infection the mock treated, infected and infected +betamethasone treated HBEC ALI-cultures were washed three times on both sides with PBS. The HBEC ALI-cultures were then lysed and RNA extraction was done using the NucleoSpin RNA II kit (Macherey-Nagel) following the manufacturer’s instructions. RNA-seq libraries were prepared using the Smart-seq2 method SARS-CoV-2 infection: The clinical isolate SARS-CoV 2/01/human/2020/SWE (GeneBank accession no. MT093571.1) was kindly provided by the Public Health Agency of Sweden. Vero E6 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) supplemented with 5% FBS (HyClone), 100 U/mL penicillin and 100 µg/ml streptomycin (PeSt, HyClone) at 37°C in 5% CO2. Propagation of the virus was done once in Vero E6 cells for 72 h and titration was done by plaque assay. The apical side of the HBEC ALI-cultures were rinsed three times with warm PBS shortly before infection. 15000 plaque forming units (PFU) of SARS-CoV-2 was added to the apical compartment in a total volume of 100µl infection medium (DMEM/PeSt), corresponding to an approximate multiplicity of infection (MOI) of 0.05. The HBEC ALI cultures were incubated at 37°C and 5% CO2 for 2.5 h before the inoculum was removed and the cultures were washed with PBS to remove residual medium.

text: adult

text: wild type genotype

text: not collected

text: SARS-CoV-2 (01/human/2020/SWE)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens


text: public

text: ArrayExpress

text: lung fibroblast

text: not collected

text: human

characteristic: common name

text: Protocols: HBECs were grown and differentiated at an air-liquid interface (ALI) forming an in vitro 3D-lung model. In short, HBECs were grown and differentiated on 6.5 mm semipermeable transwell inserts (0.4 µm Pore Polyester Membrane Insert, Corning) and after two weeks at air-liquid interface (ALI) the cultures reached full differentiation, which was assessed using light microscopy focusing on epithelial morphology, presence of ciliated cells, and mucus production along with immunofluorescence staining for ciliated cells (acetylated-tubulin, T6793, Sigma) and goblet cells (muc5AC, Ab-1 (45M1), #MS-145-P, ThermoFisher). Primary human bronchial epithelial cells (HBEC) were isolated from proximal airway tissue obtained with informed consent from a patient. At 96 h post infection the mock treated, infected and infected +betamethasone treated HBEC ALI-cultures were washed three times on both sides with PBS. The HBEC ALI-cultures were then lysed and RNA extraction was done using the NucleoSpin RNA II kit (Macherey-Nagel) following the manufacturer’s instructions. RNA-seq libraries were prepared using the Smart-seq2 method SARS-CoV-2 infection: The clinical isolate SARS-CoV 2/01/human/2020/SWE (GeneBank accession no. MT093571.1) was kindly provided by the Public Health Agency of Sweden. Vero E6 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma) supplemented with 5% FBS (HyClone), 100 U/mL penicillin and 100 µg/ml streptomycin (PeSt, HyClone) at 37°C in 5% CO2. Propagation of the virus was done once in Vero E6 cells for 72 h and titration was done by plaque assay. The apical side of the HBEC ALI-cultures were rinsed three times with warm PBS shortly before infection. 15000 plaque forming units (PFU) of SARS-CoV-2 was added to the apical compartment in a total volume of 100µl infection medium (DMEM/PeSt), corresponding to an approximate multiplicity of infection (MOI) of 0.05. The HBEC ALI cultures were incubated at 37°C and 5% CO2 for 2.5 h before the inoculum was removed and the cultures were washed with PBS to remove residual medium. Betamethasone: Fully differentiated HBEC-ALI cultures were either mock treated or treated with betamethasone (Alfasigma) 20 h prior to infection by addition of 700 µl fresh basal media containing 0.3 µM betamethasone. Shortly before infection, the basal media was exchanged once more and betamethasone was replenished in the treated wells. Betamethasone was replenished every 24 h post infection.

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: SARS-CoV-2 (01/human/2020/SWE)

characteristic: infect

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

characteristic: title


text: University of Louisville

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:313-83804

tag: Namespace:University of Louisville

characteristic: Submitter Id

characteristic: collection date

text: house mouse

text: USA

characteristic: geographic location (country and/or sea)

text: Mus musculus

text: Mus musculus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83805

text: house mouse

text: USA

text: Mus musculus

characteristic: organism

text: Mus musculus


text: University of Louisville

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83806

text: house mouse

characteristic: common name

characteristic: description

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83807

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83808

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83809

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83810

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83811

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83812

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83813

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83814

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: University of Louisville

text: public

text: ena-SAMPLE-TAB-28-09-2023-23:45:43:314-83815

text: house mouse

text: USA

text: Mus musculus

text: Mus musculus


text: public

tag: Namespace:National Institute of Biomedical Innovation, Health and Nutrition

text: human

text: scRNAseq CHB donor

text: Japan

text: Homo sapiens

text: Homo sapiens


text: National Institute of Biomedical Innovation, Health and Nutrition

text: public

text: human

text: scRNAseq CHB donor

text: Japan

text: Homo sapiens

text: Homo sapiens


E-MTAB-13373:Human iPSCs 1

text: public

text: E-MTAB-13373:Human iPSCs 1

tag: Namespace:Ludwig-Maximilians-Universität, Munich Faculty of Biology Anthropology and Human Genomics

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: not collected

text: human

text: Protocols: Previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009, Ohnuki et al. 2014). Briefly, iPSCs were dissociated and 9000 iPSCs were seeded in a low attachment U-bottom 96-well-plate in 8GMK medium consisting of GMEM (Thermo Fisher), 8% KSR (Thermo Fisher), 5.5 ml 100× NEAA (Thermo Fisher), 100 mM Sodium Pyruvate (Thermo Fisher), 50 mM 2-Mercaptoethanol (Thermo Fisher) supplemented with 500 nM A-83–01 (Sigma Aldrich), 100 nM LDN 193189 (Sigma Aldrich) and 30 µM Y27632 (biozol). Culture medium of the spheres was changed every second day until they were harvested or plated for further culture. In order to obtain stable NPC lines, spheres were dissociated on day 7 of the differentiation process using Accumax (Sigma Aldrich) and plated onto Geltrex (Thermo Fisher) coated dishes. NPCs were subsequently cultured in NPC proliferation medium (DMEM F12 (Fisher Scientific) supplemented with 2 mM GlutaMAX-I (Fisher Scientific), 20 ng/mL bFGF (Peprotech), 20 ng/mL hEGF (Miltenyi Biotec), 2% B-27 supplement (50×) minus vitamin A (Gibco), 1% N2 supplement 100× (Gibco), 200 µM L-ascorbic acid 2-phosphate (Sigma), and 100U/ml 100µg/ml penicillin-streptomycin). All cell lines have been authenticated using RNA sequencing (RNA-seq) (Geuder et al. 2021), and the current study. iPSCs of 2 clones from 2 human individuals and 2 clones of 2 cynomolgus macaque individuals were differentiated using the protocol as described above. The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. After cells were counted, 100,000 cells were pelleted at 500 rcf for 5 min, washed with 1 ml PBS and pelleted at 500 rcf for 5 min at 4 °C. The supernatant was removed completely and cells were resuspended in 100 µl chilled nuclei lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2 in water, supplemented with 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin and 1% BSA) by pipetting up and down three times, followed by incubation on ice for 3 min. After lysis, 1 ml of lysis wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2 in water, supplemented with 0.1% Tween-20 and 1% BSA) was added, and tubes were inverted three times. After counting, 50,000 nuclei were pelleted at 500 rcf for 10 min at 4°C, the supernatant was removed and nuclei were resuspended in 50 µl transposition mix (25 µl 2x TD buffer, 2.5 µl TDE1, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20 and 5 µl ddH2O) by pipetting six times. Transposition reactions were incubated at 37 °C for 1 h at 1000 rpm shaking, followed by a clean-up using the DNA Clean & Concentrator-5 kit (Zymo). For library generation, 20 µl of the transposed sample was mixed with 2.5 µl 25µl p5 custom primer, 2.5 µl 25µl p7 custom primer from Buenrostro et al. 2013 and 25 µl NEBNext Ultra II Q5 2x Master Mix (NEB) and a PCR with 10 cycles was conducted as stated in the Omni-ATAC protocol. Libraries were purified using the DNA Clean & Concentrator-5 kit, run on a 2% E-Gel (Thermo Fisher) and gel excision of DNA between 150 bp and 1,500 bp was performed using the Monarch DNA Gel Excision Kit (NEB).

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: Human iPSCs 1


E-MTAB-13373:Human iPSCs 2

text: Ludwig-Maximilians-Universität, Munich Faculty of Biology Anthropology and Human Genomics

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-13373:Human iPSCs 2

text: ArrayExpress

text: induced pluripotent stem cell

text: not collected

text: human

text: wild type genotype

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens

text: Human iPSCs 2

characteristic: title


E-MTAB-13373:Human NPCs 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-13373:Human NPCs 1

characteristic: Submitter Id

text: ArrayExpress

text: neural progenitor cell

text: not collected

characteristic: collection date

text: human

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens

text: Human NPCs 1


E-MTAB-13373:Human NPCs 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-13373:Human NPCs 2

text: ArrayExpress

text: neural progenitor cell

text: not collected

text: human

text: wild type genotype

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens

text: Human NPCs 2


E-MTAB-13373:Macaque iPSCs 1

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13373:Macaque iPSCs 1

text: ArrayExpress

text: induced pluripotent stem cell

text: not collected

text: crab-eating macaque

characteristic: common name

characteristic: description

text: wild type genotype

text: not collected

text: not applicable

text: Macaca fascicularis

text: Macaca fascicularis

text: induced pluripotent stem cell

text: Macaca fascicularis

text: Macaque iPSCs 1


E-MTAB-13373:Macaque iPSCs 2

text: public

text: E-MTAB-13373:Macaque iPSCs 2

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: not collected

text: crab-eating macaque

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Macaca fascicularis

text: Macaca fascicularis

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: Macaca fascicularis

text: Macaque iPSCs 2


E-MTAB-13373:Macaque NPCs 1

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-13373:Macaque NPCs 1

text: ArrayExpress

text: neural progenitor cell

text: not collected

text: crab-eating macaque

text: wild type genotype

text: not collected

text: not applicable

text: Macaca fascicularis

text: Macaca fascicularis

text: induced pluripotent stem cell

text: Macaca fascicularis

text: Macaque NPCs 1

characteristic: title


E-MTAB-13373:Macaque NPCs 2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-13373:Macaque NPCs 2

characteristic: Submitter Id

text: ArrayExpress

text: neural progenitor cell

text: not collected

characteristic: collection date

text: crab-eating macaque

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Macaca fascicularis

text: Macaca fascicularis

text: induced pluripotent stem cell

text: Macaca fascicularis

text: Macaque NPCs 2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY

text: Japan

text: Pristionchus sp. 7 TWN1156

characteristic: organism

text: Pristionchus sp. 7 TWN1156


text: MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: description

text: Japan

text: Pristionchus sp. 7 TWN1156

text: Pristionchus sp. 7 TWN1156


text: The University of Edinburgh

text: public

tag: Namespace:The University of Edinburgh

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

text: Protocols: Salivary gland tissue was excised, enzymatically and mechanically digested and Epcam+ cells (epithelial cells), CD31+ cells (endothelial cells) and CD45+/CD11b+/F480+ cells (macrophages) were isolated using fluorescence-activated cell sorting (FACS) and mixed in the ratio 45%, 45%, 10%, respectively. Isolated cells were loaded into the Chromium Single Cell controller (10x Genomics). Nucleic acid extraction was performed following the manufacturer's instructions (10x Genomics, as part of the Chromium Single Cell 3' v3.1). The four libraries (one for each sample) were pooled for sequencing, taking into account the expected differences in cell numbers between each library.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: 1340855 and 1340856

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: submandibular gland

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The University of Edinburgh

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: 1340832 and 1340834

text: not applicable

text: Mus musculus

text: Mus musculus

text: submandibular gland

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Edinburgh

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

text: not collected

text: 1340825 and 1340826

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: submandibular gland

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The University of Edinburgh

text: public

text: ArrayExpress

text: not collected

text: house mouse

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: 1340829 and 1340830

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: submandibular gland

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universita degli studi di Milano

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Universita degli studi di Milano

characteristic: Submitter Id

characteristic: collection date

text: SampleName_SubjectName_Group_Treatment_Time

text: Italy

characteristic: geographic location (country and/or sea)

text: bacterium

text: bacterium

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Statens Serum Institut

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Statens Serum Institut

text: building

characteristic: broad-scale environmental context

characteristic: depth

text: wastewater

characteristic: environmental medium

text: Denmark

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: wastewater treatment plant

characteristic: local environmental context

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: SARS-CoV-2 wastewater Illumina sequencing, Denmark

characteristic: project name

text: Illumina

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

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

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COVID-19 Genomics UK Consortium

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: title

text: not provided


text: public

tag: Namespace:Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: Wales

characteristic: geographic location (region and locality)

text: not provided

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

characteristic: host subject id

text: not provided

characteristic: isolate

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: Wales

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


text: public

tag: Namespace:Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17792/2023

characteristic: organism

text: active surveillance not initiated by an outbreak

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17803/2023

characteristic: isolate


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17795/2023

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17793/2023

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17776/2023

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17782/2023

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17798/2023

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17797/2023

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17796/2023

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17811/2023

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17778/2023

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17808/2023

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17810/2023

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Hôpital Cantonal de Fribourg - HFR, CH-1752 Villars-sur-Glâne, Switzerland

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

text: Switzerland

text: VD

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/VD-CHUV-GEN17790/2023

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17800/2023

text: active surveillance not initiated by an outbreak

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17813/2023

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17801/2023

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17799/2023

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17781/2023

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17779/2023

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17807/2023

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17805/2023

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17812/2023

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17791/2023

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17783/2023

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17787/2023

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17794/2023

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17806/2023

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17809/2023

characteristic: isolate

text: active surveillance not initiated by an outbreak


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Hôpital Cantonal de Fribourg - HFR, CH-1752 Villars-sur-Glâne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17786/2023

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17777/2023

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

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/VD-CHUV-GEN17775/2023

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17802/2023

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN17804/2023

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SIB

text: Switzerland

text: VD

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/VD-CHUV-GEN17784/2023

characteristic: isolate


E-MTAB-13377:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-13377:Sample 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: pluripotent

characteristic: chondrogenic differentiation

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: Briefly, adherent cells were dissociated, harvested and centrifuged at 16,000xg. The cell pellet was then resuspended in 300μl lysis buffer. Cell lysate was then transferred to a gDNA removal column and spun at 16,000xg for 30 seconds to remove genomic DNA. The flow-through was collected and RNA was precipitated with the addition of 300μl pure ethanol (≥95%). Total RNA was then transferred to an RNA purification column and subjected to a series of on-column washes and centrifugations before elution in nuclease-free water (Invitrogen, #4387937) according to the manufacturer’s instructions. This submission contains human embryonic stem cells (hESCs) and differentiated samples. An optogenetic bone morphogenetic protein (BMP) signalling system (optoBMP) was used to drive chondrogenic differentiation of human embryonic stem cells (hESCs). The human embryonic stem cell line MAN13 is a clinical grade hESC line which has been well characterised (PMID: 28583200) (https://hpscreg.eu/cell-line/UMANe002-A) and was derived under local ethical approval (Central Manchester LREC favourable opinion 03/CM/684) and UK Human Fertilisation and Embryology Authority license (HFEA licence R0171) with fully informed parental consent. Here MAN13 was modified with an optogenetic BMP signalling system that functions through light-induced dimerisation of light-oxygen-voltage (LOV) domains fused to the intracellular regions of BMPR1B/ALK6 and BMPR2 (Humphreys, P. A., Woods, S., Smith, C. A., Bates, N., Cain, S. A., Lucas, R. & Kimber, S. J. Optogenetic control of the BMP signaling pathway. ACS Synthetic Biology 9, 3067–3078 (2020)). Samples for RNA-seq analysis of optoBMP-hESC-derived chondroprogenitors were collected at day 11 after differentiation with either light (LIGHT), a combination of BMP2 and GDF5 (B2/G5) or after being kept in dark conditions without additional BMP pathway activation (DARK). OptoMAN13 were subjected to chondrogenic differentiation as previously described (Mancini, F. E., Humphreys, P. E. A., Woods, S., Bates, N., Cuvertino, S., O’Flaherty, J., Biant, L., Domingos, M. A. N. & Kimber, S. J. Effect of a retinoic acid analogue on BMP-driven pluripotent stem cell chondrogenesis. bioRxiv (2023). at <https://doi.org/10.1101/2023.06.20.545738>). OptoMAN13 cells were seeded in 24 well plates at 5x104 cells/well and maintained in dark conditions prior to optogenetic stimulation. Optical stimulation was performed using a custom-built Arduino-controlled LED array device using blue 488nm LEDs within a standard cell culture incubator at 37°C (5% Co2, 20% O2). Optogenetic stimulation was achieved by intermittent illumination of optoMAN13 cells (1 hour illumination, 3 hours dark) at 1.5mW/cm2 irradiance. Total RNA was extracted using Monarch® Total RNA Miniprep Kit (New England Biolabs inc. #T2010S) following manufacturer protocol. Stranded mRNA protocol

characteristic: description

text: embryo

characteristic: developmental stage

text: not collected

characteristic: geographic location (country and/or sea)

text: dark

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: stimulus

text: Sample 1


E-MTAB-13377:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13377:Sample 10

text: ArrayExpress

text: differentiated

text: not collected

text: human

text: embryo

text: not collected

text: dark

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 10

characteristic: title


E-MTAB-13377:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-13377:Sample 11

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: differentiated

characteristic: chondrogenic differentiation

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: dark

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 11


E-MTAB-13377:Sample 12

characteristic: ENA-LAST-UPDATE

text: UOM

text: public

text: E-MTAB-13377:Sample 12

text: ArrayExpress

text: differentiated

text: not collected

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: not collected

characteristic: geographic location (country and/or sea)

text: dark

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: stimulus

text: Sample 12


E-MTAB-13377:Sample 2

characteristic: External Id

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13377:Sample 2

text: ArrayExpress

text: pluripotent

text: not collected

text: human

text: embryo

text: not collected

text: dark

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-13377:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-13377:Sample 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: pluripotent

characteristic: chondrogenic differentiation

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: dark

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 3


E-MTAB-13377:Sample 4

characteristic: ENA-LAST-UPDATE

text: UOM

text: public

text: E-MTAB-13377:Sample 4

text: ArrayExpress

text: differentiated

text: not collected

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: not collected

characteristic: geographic location (country and/or sea)

text: blue light exposure

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: light-induced BMP signalling pathway activation

characteristic: stimulus

text: Sample 4


E-MTAB-13377:Sample 5

characteristic: External Id

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13377:Sample 5

text: ArrayExpress

text: differentiated

text: not collected

text: human

text: embryo

text: not collected

text: blue light exposure

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 5

characteristic: title


E-MTAB-13377:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-13377:Sample 6

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: differentiated

characteristic: chondrogenic differentiation

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: blue light exposure

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 6


E-MTAB-13377:Sample 7

characteristic: ENA-LAST-UPDATE

text: UOM

text: public

text: E-MTAB-13377:Sample 7

text: ArrayExpress

text: differentiated

text: not collected

text: human

characteristic: description

text: embryo

characteristic: developmental stage

text: not collected

characteristic: geographic location (country and/or sea)

text: dark

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

characteristic: organism part

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: gdf5 growth factor (20 ng/ml) and bmp2 growth factor (25 ng/ml)

characteristic: stimulus

text: Sample 7


E-MTAB-13377:Sample 8

characteristic: External Id

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13377:Sample 8

text: ArrayExpress

text: differentiated

text: not collected

text: human

text: embryo

text: not collected

text: dark

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 8

characteristic: title


E-MTAB-13377:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UOM

text: public

text: E-MTAB-13377:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: differentiated

characteristic: chondrogenic differentiation

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: dark

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: embryonic tissue

text: embryonic stem cell

text: Homo sapiens

text: Sample 9


unit: ng/ul

characteristic: DNA quantification Qubit

characteristic: ENA-LAST-UPDATE

text: CHUV-UNIL

text: public

text: host-associated environment

characteristic: broad-scale environmental context

characteristic: cage

text: feces

characteristic: environmental medium

characteristic: experiment

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: WT

characteristic: group

text: faecal pellets

characteristic: host body product

text: Mouse

characteristic: host common name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host subspecific genetic lineage

characteristic: host taxid

characteristic: line

text: intestine environment

characteristic: local environmental context

characteristic: mutation

text: Qiagen Microbial DNA-Free Water

characteristic: negative control type

text: mouse gut metagenome

text: forward: CCTACGGGNGGCWGCAG, reverse: GACTACHVGGGTATCTAATCC

characteristic: pcr primers

text: 20 Strain Even Mix Whole Cell Material MSA-2002

characteristic: positive control type

text: REPAGE

characteristic: project name

unit: months

characteristic: sample storage duration

unit: °C

characteristic: sample storage temperature

text: mouse gut metagenome

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: Mouse fecal microbiota R_12403_D0


characteristic: DNA quantification Qubit

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHUV-UNIL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: host-associated environment

characteristic: broad-scale environmental context

characteristic: cage

characteristic: collection date

text: feces

characteristic: environmental medium

characteristic: experiment

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: WT

characteristic: group

text: faecal pellets

characteristic: host body product

text: Mouse

text: male

text: intestine environment

text: Qiagen Microbial DNA-Free Water

text: mouse gut metagenome

characteristic: organism

text: REPAGE

text: mouse gut metagenome

text: 16S rRNA

text: Mouse fecal microbiota R_12403_D2

characteristic: title


characteristic: DNA quantification Qubit

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHUV-UNIL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: host-associated environment

text: feces

text: Switzerland

text: WT

text: faecal pellets

text: Mouse

characteristic: host common name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host subspecific genetic lineage

characteristic: host taxid

characteristic: line

text: intestine environment

characteristic: local environmental context

characteristic: mutation

text: Qiagen Microbial DNA-Free Water

characteristic: negative control type

text: mouse gut metagenome

characteristic: pcr primers

characteristic: positive control type

text: REPAGE

characteristic: project name

characteristic: sample storage duration

characteristic: sample storage temperature

text: mouse gut metagenome

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: Mouse fecal microbiota R_12403_D4


characteristic: DNA quantification Qubit

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHUV-UNIL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: host-associated environment

characteristic: broad-scale environmental context

characteristic: cage

characteristic: collection date

text: feces

characteristic: environmental medium

characteristic: experiment

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: WT

characteristic: group

text: faecal pellets

characteristic: host body product

text: Mouse

text: male

text: intestine environment

text: Qiagen Microbial DNA-Free Water

text: mouse gut metagenome

characteristic: organism

text: REPAGE

text: mouse gut metagenome

text: 16S rRNA

text: Mouse fecal microbiota R_12429_D0

characteristic: title


characteristic: DNA quantification Qubit

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CHUV-UNIL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: host-associated environment

text: feces

text: Switzerland

text: WT

text: faecal pellets

text: Mouse

characteristic: host common name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host subspecific genetic lineage

characteristic: host taxid

characteristic: line

text: intestine environment

characteristic: local environmental context

characteristic: mutation

text: Qiagen Microbial DNA-Free Water

characteristic: negative control type

text: mouse gut metagenome

characteristic: pcr primers

characteristic: positive control type

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characteristic: DNA quantification Qubit

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