E-MTAB-11942:Sample 6

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11942:Sample 6

characteristic: Submitter Id

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text: ArrayExpress

characteristic: broker name

text: bone marrow cell

characteristic: cell type

text: human

characteristic: description

text: adult

text: aplastic anemia

text: East Asian

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: Sample 6


E-MTAB-11942:Sample 7

status: PUBLIC

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text: public

characteristic: INSDC status

text: E-MTAB-11942:Sample 7

tag: Namespace:State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China

unit: year

text: ArrayExpress

text: bone marrow cell

text: human

characteristic: common name

text: Protocols: BM nucleated cells (BMNCs) from healthy donors and patients with NSAA at the time of initial diagnosis were separated, and then co-cultured with or without 40 μg/mL LMS for 48 hours in vitro. Cells were harvested and total RNA were extracted. Total RNA after different treatments was extracted using Trizol as described by the manufacturer’s protocol. The assay were carried out using the Illumina HiSeq X platform and the data obtained were analyzed by following the Hisat2 protocol.

text: adult

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text: aplastic anemia

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text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 7

characteristic: title


E-MTAB-11942:Sample 8

text: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China

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text: public

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text: human

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text: adult

text: aplastic anemia

text: East Asian

text: not applicable

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characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: Sample 8


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text: public

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

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

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


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text: ETH Zurich

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text: E-MTAB-11939:Bovine_Donor1_24hpi_33C_ICV

tag: Namespace:University of Bern Institute for Infectious Diseases

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text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: common name

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bern Institute for Infectious Diseases

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_24hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor1_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


text: public

text: E-MTAB-11939:Bovine_Donor1_24hpi_37C_ICV

text: ArrayExpress

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor1_24hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_24hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor1_48hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor1_48hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor1_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_48hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor1_48hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor1_48hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor1_72hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_72hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor1_72hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor1_72hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor1_72hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bern Institute for Infectious Diseases

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_72hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor1_96hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor1_96hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor1_96hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor1_96hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor1_96hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor1_96hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_24hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_24hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor2_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor2_24hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_24hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_24hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor2_48hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor2_48hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


text: University of Bern Institute for Infectious Diseases

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_48hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor2_48hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor2_48hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_72hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_72hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor2_72hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor2_72hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_72hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_72hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor2_96hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor2_96hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor2_96hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor2_96hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor2_96hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor2_96hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_24hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Bern Institute for Infectious Diseases

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor3_24hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor3_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor3_24hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_24hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: ENA-LAST-UPDATE

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text: public

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text: E-MTAB-11939:Bovine_Donor3_24hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC center name

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text: public

text: E-MTAB-11939:Bovine_Donor3_48hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor3_48hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor3_48hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor3_48hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor3_48hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_72hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor3_72hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor3_72hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor3_72hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_72hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: IDV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bern Institute for Infectious Diseases

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor3_72hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: Mock

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Bovine_Donor3_96hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor3_96hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Bovine_Donor3_96hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: replicate

text: Bos taurus

text: Mock

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Bovine_Donor3_96hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

text: not applicable

text: Bos taurus

characteristic: organism

text: Bos taurus

text: respiratory system

text: Bos taurus

text: ICV

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Bovine_Donor3_96hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: cattle

characteristic: description

text: not applicable

text: Bos taurus

text: Bos taurus

text: respiratory system

text: Bos taurus

text: IDV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Bovine_Donor3_96hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: cattle

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Bos taurus

text: Bos taurus

text: respiratory system

characteristic: organism part

text: Bos taurus

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: replicate

text: Homo sapiens

text: ICV

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: IDV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Human_Donor1_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

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text: respiratory epithelial cell

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text: human

characteristic: description

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Human_Donor1_24hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: organism part

text: Homo sapiens

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Human_Donor1_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: replicate

text: Homo sapiens

text: Mock

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

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text: E-MTAB-11939:Human_Donor1_48hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Human_Donor1_72hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

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text: respiratory epithelial cell

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text: human

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text: not applicable

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text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Human_Donor1_72hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

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text: not applicable

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text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: organism part

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text: Mock


characteristic: ENA-LAST-UPDATE

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characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Human_Donor1_96hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: replicate

text: Homo sapiens

text: Mock

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Human_Donor1_96hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Human_Donor2_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: human

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

characteristic: description

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bern Institute for Infectious Diseases

text: public

text: E-MTAB-11939:Human_Donor2_24hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

characteristic: common name

characteristic: growth condition

text: not applicable

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text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: organism part

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text: Mock


characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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text: E-MTAB-11939:Human_Donor2_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

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text: Homo sapiens

text: respiratory system

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text: Homo sapiens

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characteristic: INSDC center name

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text: primary cell line

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text: human

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock

characteristic: title


characteristic: ENA-CHECKLIST

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text: E-MTAB-11939:Human_Donor3_48hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: human

characteristic: description

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Human_Donor3_48hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: organism part

text: Homo sapiens

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Human_Donor3_72hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: replicate

text: Homo sapiens

text: Mock

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Human_Donor3_72hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Human_Donor3_96hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: human

characteristic: description

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: respiratory system

text: Homo sapiens

text: Mock


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Human_Donor3_96hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: human

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: respiratory system

characteristic: organism part

text: Homo sapiens

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_24hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: ICV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Bern Institute for Infectious Diseases

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_24hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: IDV

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Porcine_Donor1_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Porcine_Donor1_24hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: ICV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_24hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: IDV

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_24hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: Mock

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Porcine_Donor1_48hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: ICV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Porcine_Donor1_48hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: IDV


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_48hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: Mock

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_48hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: ICV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Porcine_Donor1_48hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: IDV


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Porcine_Donor1_48hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_72hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: ICV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_72hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: IDV

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Porcine_Donor1_72hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Porcine_Donor1_72hpi_37C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: ICV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_72hpi_37C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: Protocols: We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq). Virus-infected and control hAEC cultures were lyzed with 350 uL of MR1 lysis buffer from NucleoMag RNA kit(Macherey-Nagel) according manufacturers guidelines, samples were stored at -80°C for later analysis. Cell lysates were collected at 24, 48, 72, and 96 hpi from cultures  incubated at 33°C and 37°C. Isolation and culturing of primary material was performed as previously described (Gultom, M., Laloli, L. & Dijkman, R. Well-Differentiated Primary Mammalian Airway Epithelial Cell Cultures. in Methods in Molecular Biology 2203, 119–134). Until the experimental procedures, all AEC cultures were maintained at 37°C in a humidified incubator with 5% CO2. Total cellular RNA from mock and virus-infected hAEC cultures was extracted with the NucleoMag RNA kit (Macherey-Nagel) according manufacturers guidelines on a Kingfisher Flex Purification system (Thermofisher). Total RNA concentration was quantified with QuantiFluor® RNA System (Promega) according manufactures guidelines on a Cytation 5 multimode reader (Biotek). BRB-seq protocol (Alpern, D., Gardeux, V., Russeil, J. et al. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome Biol 20, 71 (2019). https://doi.org/10.1186/s13059-019-1671-x)

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: IDV

characteristic: strain


text: University of Bern Institute for Infectious Diseases

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_72hpi_37C_Mock

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: Mock

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11939:Porcine_Donor1_96hpi_33C_ICV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: ICV


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Porcine_Donor1_96hpi_33C_IDV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: IDV


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor1_96hpi_33C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: Mock

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor1_96hpi_37C_ICV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: ICV

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11939:Porcine_Donor1_96hpi_37C_IDV

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: IDV


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Porcine_Donor1_96hpi_37C_Mock

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

characteristic: common name

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: organism part

text: Sus scrofa

text: Mock


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11939:Porcine_Donor2_24hpi_33C_ICV

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

characteristic: replicate

text: Sus scrofa

text: ICV

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11939:Porcine_Donor2_24hpi_33C_IDV

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: respiratory epithelial cell

text: pig

text: not applicable

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: IDV

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11939:Porcine_Donor2_24hpi_33C_Mock

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: respiratory epithelial cell

characteristic: cell type

text: pig

characteristic: description

text: not applicable

text: Sus scrofa

text: Sus scrofa

text: respiratory system

text: Sus scrofa

text: Mock