ERS11915725 SAMEA14321604 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321604 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S506 age 75 alt_well_id a11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N701_S506 sample_series nine_ind sex female ERS11915726 SAMEA14321605 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321605 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S507 age 75 alt_well_id a12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N701_S507 sample_series nine_ind sex female ERS11915727 SAMEA14321606 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321606 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S506 age 70 alt_well_id b11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N702_S506 sample_series nine_ind sex female ERS11915728 SAMEA14321607 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321607 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S507 age 70 alt_well_id b12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N702_S507 sample_series nine_ind sex female ERS11915729 SAMEA14321608 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321608 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S506 age 70 alt_well_id c11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N703_S506 sample_series nine_ind sex male ERS11915730 SAMEA14321609 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA-FIRST-PUBLIC 2022-05-05T00:16:07Z ENA-LAST-UPDATE 2022-05-05T00:16:07Z External Id SAMEA14321609 INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S507 age 70 alt_well_id c12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N703_S507 sample_series nine_ind scientific_name Homo sapiens sex male ERS11915731 SAMEA14321610 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321610 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S506 age 70 alt_well_id e11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N705_S506 sample_series nine_ind sex male ERS11915732 SAMEA14321611 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321611 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S507 age 70 alt_well_id e12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N705_S507 sample_series nine_ind sex male ERS11915733 SAMEA14321612 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321612 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S506 age 70 alt_well_id f11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N706_S506 sample_series nine_ind sex male ERS11915734 SAMEA14321613 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321613 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S507 age 70 alt_well_id f12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N706_S507 sample_series nine_ind sex male ERS11915735 SAMEA14321614 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321614 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S506 age 70 alt_well_id k11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N707_S506 sample_series nine_ind sex female ERS11915736 SAMEA14321615 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321615 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S507 age 70 alt_well_id k12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N707_S507 sample_series nine_ind sex female ERS11915737 SAMEA14321616 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321616 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S506 age 75 alt_well_id l11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N708_S506 sample_series nine_ind sex female ERS11915738 SAMEA14321617 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321617 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S507 age 75 alt_well_id l12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N708_S507 sample_series nine_ind sex female ERS11915739 SAMEA14321618 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321618 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S506 age 60 alt_well_id m11 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N709_S506 sample_series nine_ind sex male ERS11915740 SAMEA14321619 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321619 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S507 age 60 alt_well_id m12 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N709_S507 sample_series nine_ind sex male ERS11915741 SAMEA14321620 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321620 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S503 age 75 alt_well_id a5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N701_S503 sample_series nine_ind sex female ERS11915742 SAMEA14321621 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321621 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S504 age 75 alt_well_id a6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N701_S504 sample_series nine_ind sex female ERS11915743 SAMEA14321622 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321622 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S503 age 70 alt_well_id b5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N702_S503 sample_series nine_ind sex female ERS11915744 SAMEA14321623 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321623 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S504 age 70 alt_well_id b6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N702_S504 sample_series nine_ind sex female ERS11915745 SAMEA14321624 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321624 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S503 age 70 alt_well_id c5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N703_S503 sample_series nine_ind sex male ERS11915746 SAMEA14321625 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321625 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S504 age 70 alt_well_id c6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N703_S504 sample_series nine_ind sex male ERS11915747 SAMEA14321626 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321626 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N704_S503 age 70 alt_well_id d5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual d infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N704_S503 sample_series nine_ind sex male ERS11915748 SAMEA14321627 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321627 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N704_S504 age 70 alt_well_id d6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual d infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N704_S504 sample_series nine_ind sex male ERS11915749 SAMEA14321628 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321628 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S503 age 70 alt_well_id e5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N705_S503 sample_series nine_ind sex male ERS11915750 SAMEA14321629 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321629 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S504 age 70 alt_well_id e6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N705_S504 sample_series nine_ind sex male ERS11915751 SAMEA14321630 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321630 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S503 age 70 alt_well_id f5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N706_S503 sample_series nine_ind sex male ERS11915752 SAMEA14321631 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321631 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S504 age 70 alt_well_id f6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N706_S504 sample_series nine_ind sex male ERS11915753 SAMEA14321632 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321632 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S503 age 70 alt_well_id k5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N707_S503 sample_series nine_ind sex female ERS11915754 SAMEA14321633 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321633 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S504 age 70 alt_well_id k6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N707_S504 sample_series nine_ind sex female ERS11915755 SAMEA14321634 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321634 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S503 age 75 alt_well_id l5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N708_S503 sample_series nine_ind sex female ERS11915756 SAMEA14321635 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321635 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S504 age 75 alt_well_id l6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N708_S504 sample_series nine_ind sex female ERS11915757 SAMEA14321636 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321636 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S503 age 60 alt_well_id m5 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N709_S503 sample_series nine_ind sex male ERS11915758 SAMEA14321637 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321637 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S504 age 60 alt_well_id m6 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m infect Severe acute respiratory syndrome coronavirus 2 organism part lung sample name E-MTAB-10687:N709_S504 sample_series nine_ind sex male ERS11915759 SAMEA14321638 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321638 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S505 age 75 alt_well_id a8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a organism part lung sample name E-MTAB-10687:N701_S505 sample_series nine_ind sex female ERS11915760 SAMEA14321639 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321639 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S505 age 70 alt_well_id b8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b organism part lung sample name E-MTAB-10687:N702_S505 sample_series nine_ind sex female ERS11915761 SAMEA14321640 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321640 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S505 age 70 alt_well_id c8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c organism part lung sample name E-MTAB-10687:N703_S505 sample_series nine_ind sex male ERS11915762 SAMEA14321641 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321641 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N704_S505 age 70 alt_well_id d8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual d organism part lung sample name E-MTAB-10687:N704_S505 sample_series nine_ind sex male ERS11915763 SAMEA14321642 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321642 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S505 age 70 alt_well_id e8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e organism part lung sample name E-MTAB-10687:N705_S505 sample_series nine_ind sex male ERS11915764 SAMEA14321643 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321643 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S505 age 70 alt_well_id f8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f organism part lung sample name E-MTAB-10687:N706_S505 sample_series nine_ind sex male ERS11915765 SAMEA14321644 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321644 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S505 age 70 alt_well_id k8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k organism part lung sample name E-MTAB-10687:N707_S505 sample_series nine_ind sex female ERS11915766 SAMEA14321645 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321645 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S505 age 75 alt_well_id l8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l organism part lung sample name E-MTAB-10687:N708_S505 sample_series nine_ind sex female ERS11915767 SAMEA14321646 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321646 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S505 age 60 alt_well_id m8 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m organism part lung sample name E-MTAB-10687:N709_S505 sample_series nine_ind sex male ERS11915768 SAMEA14321647 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321647 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N701_S502 age 75 alt_well_id a2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual a organism part lung sample name E-MTAB-10687:N701_S502 sample_series nine_ind sex female ERS11915769 SAMEA14321648 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321648 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N702_S502 age 70 alt_well_id b2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual b organism part lung sample name E-MTAB-10687:N702_S502 sample_series nine_ind sex female ERS11915770 SAMEA14321649 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321649 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N703_S502 age 70 alt_well_id c2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual c organism part lung sample name E-MTAB-10687:N703_S502 sample_series nine_ind sex male ERS11915771 SAMEA14321650 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321650 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N704_S502 age 70 alt_well_id d2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual d organism part lung sample name E-MTAB-10687:N704_S502 sample_series nine_ind sex male ERS11915773 SAMEA14321652 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321652 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N706_S502 age 70 alt_well_id f2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual f organism part lung sample name E-MTAB-10687:N706_S502 sample_series nine_ind sex male ERS11915774 SAMEA14321653 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321653 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N707_S502 age 70 alt_well_id k2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual k organism part lung sample name E-MTAB-10687:N707_S502 sample_series nine_ind sex female ERS11915775 SAMEA14321654 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321654 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N708_S502 age 75 alt_well_id l2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual l organism part lung sample name E-MTAB-10687:N708_S502 sample_series nine_ind sex female ERS11915776 SAMEA14321655 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321655 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N709_S502 age 60 alt_well_id m2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual m organism part lung sample name E-MTAB-10687:N709_S502 sample_series nine_ind sex male ERS11915772 SAMEA14321651 9606 Homo sapiens Protocols: Primary human bronchial epithelial cells (HBEC) were isolated with informed consent from lung tissue from of patients who underwent thoracic surgery. HBEC were grown in Bronchial Epithelial Cell Medium (BEpiCM, SC3211-b, SienCell) with recommended supplements (SC3262, SienCell) and 100 U PeSt. For differentiation 0.75 x105 cells were seeded onto a 6.5 mm semipermeable transwell insert (0.4 µm Pore Polyester Membrane Insert, Corning) in differentiation media (DMEM:BEpiCM 1:1 supplemented with 52 μg/ml bovine pituitary extract, 0.5 μg/ml hydrocortisone, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 10 μg/ml transferrin, 5 μg/ml insulin, 50 nM retinoic acid (all from Sigma Aldrich) and PeSt according to (doi: 10.1152/ajplung.00311.2001. PubMed PMID: 11792627). Cells were maintained submerged for the first 7 days, after which the media was removed from the apical side and cells were grown at air-liquid interface for an additional two weeks to reach full differentiation. Media was replaced three times per week with addition of fresh retinoic acid to the media shortly before usage. Immediately prior to infection the apical side of the HBEC ALI cultures was rinsed three times with PBS. For infection, 1.5x104 PFU of SARS-CoV-2 in a total volume of 100 µl infection medium (DMEM + 100 U PeSt) was added to the apical compartment, corresponding to an approximate MOI of 0.05. Cells were incubated at 37 °C and 5 % CO2 for 2.5 h before the inoculum was removed and the cells washed with PBS to remove residual medium. 72 h.p.i the cells were washed three times with PBS and RNA was harvested from mock-infected (n=1) and infected (n=2) HBEC from individual donors using the NucleoSpin RNA II kit (Macherey-Nagel) in accordance with the manufacturer's instructions. According to smartseq2, https://www.nature.com/articles/nprot.2014.006 ENA first public 2022-05-05 ENA last update 2022-05-05 External Id SAMEA14321651 INSDC center alias Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC center name Laboratory of Molecular Infection Medicine Sweden (MIMS), Umea university INSDC first public 2022-05-05T00:16:07Z INSDC last update 2022-05-05T00:16:07Z INSDC status public Submitter Id E-MTAB-10687:N705_S502 age 70 alt_well_id e2 broker name ArrayExpress cell type bronchial epithelial cell common name human developmental stage adult individual e organism part lung sample name E-MTAB-10687:N705_S502 sample_series nine_ind sex male