Virus Expression Database

GSE147507

Transcriptional response to SARS-CoV-2 infection

Submitted by Daniel Blanco Melo (Icahn School of Medicine at Mount Sina, USA) on Apr 20 2020

Platform: ngs – Illumina NextSeq 500 (Homo sapiens)

Pubmed: 32416070, 33782412

Summary Viral pandemics pose an imminent threat to humanity. The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, requires the urgent development of anti-viral therapies. Because of its recent emergence, there is a paucity of information regarding viral behavior and host response following SARS-CoV-2 infection. Here, we offer an in-depth analysis of the host response to SARS-CoV-2 as it compares to other respiratory infections. Cell and animal models of SARS-CoV-2 infections, in addition to transcriptional profiling of a COVID-19 lung biopsy consistently revealed a unique and inappropriate inflammatory response defined by elevated chemokine expression in the absence of Type I and III interferons. Our identification of a muted transcriptional response to SARS-CoV-2 supports a model in which initial failure to rapidly respond to infection results in prolonged viral replication and an influx of proinflammatory cells that induce alveolar damage and manifest in COVID-19 lung pathology.

78 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM4432378 Series1_NHBE_Mock_1 bronchial epithelial cell  Mock Uninfected
GSM4432379 Series1_NHBE_Mock_2 bronchial epithelial cell  Mock Uninfected
GSM4432380 Series1_NHBE_Mock_3 bronchial epithelial cell  Mock Uninfected
GSM4432381 Series1_NHBE_SARS-CoV-2_1 bronchial epithelial cell  24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432382 Series1_NHBE_SARS-CoV-2_2 bronchial epithelial cell  24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432383 Series1_NHBE_SARS-CoV-2_3 bronchial epithelial cell  24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432384 Series2_A549_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432385 Series2_A549_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432386 Series2_A549_Mock_3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432387 Series2_A549_SARS-CoV-2_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432388 Series2_A549_SARS-CoV-2_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432389 Series2_A549_SARS-CoV-2_3 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4432390 Series3_A549_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432391 Series3_A549_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432392 Series3_A549_RSV_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs RSV (A2) Human orthopneumovirus
GSM4432393 Series3_A549_RSV_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs RSV (A2) Human orthopneumovirus
GSM4432394 Series4_A549_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432395 Series4_A549_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4432396 Series4_A549_IAV_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 9 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4432397 Series4_A549_IAV_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 9 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4462336 Series5_A549_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462337 Series5_A549_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462338 Series5_A549_Mock_3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462339 Series5_A549_SARS-CoV-2_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462340 Series5_A549_SARS-CoV-2_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462341 Series5_A549_SARS-CoV-2_3 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462342 Series6_A549-ACE2_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4462343 Series6_A549-ACE2_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4462344 Series6_A549-ACE2_Mock_3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4462345 Series6_A549-ACE2_SARS-CoV-2_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4462346 Series6_A549-ACE2_SARS-CoV-2_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4462347 Series6_A549-ACE2_SARS-CoV-2_3 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4462348 Series7_Calu3_Mock_1 lung adenocarcinoma cell line  [Calu-3 ] Mock Uninfected
GSM4462349 Series7_Calu3_Mock_2 lung adenocarcinoma cell line  [Calu-3 ] Mock Uninfected
GSM4462350 Series7_Calu3_Mock_3 lung adenocarcinoma cell line  [Calu-3 ] Mock Uninfected
GSM4462351 Series7_Calu3_SARS-CoV-2_1 lung adenocarcinoma cell line  [Calu-3 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462352 Series7_Calu3_SARS-CoV-2_2 lung adenocarcinoma cell line  [Calu-3 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462353 Series7_Calu3_SARS-CoV-2_3 lung adenocarcinoma cell line  [Calu-3 ] 24 hrs SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus
GSM4462354 Series8_A549_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462355 Series8_A549_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462356 Series8_A549_Mock_3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected
GSM4462357 Series8_A549_RSV_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs RSV (A2) Human orthopneumovirus
GSM4462358 Series8_A549_RSV_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs RSV (A2) Human orthopneumovirus
GSM4462359 Series8_A549_RSV_3 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs RSV (A2) Human orthopneumovirus
GSM4462360 Series8_A549_HPIV3_1 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs HPIV3 (JS) Human respirovirus 3
GSM4462361 Series8_A549_HPIV3_2 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs HPIV3 (JS) Human respirovirus 3
GSM4462362 Series8_A549_HPIV3_3 non-small cell lung adenocarcinoma cell line  [A-549 ] 24 hrs HPIV3 (JS) Human respirovirus 3
GSM4462363 Series9_NHBE_Mock_1 bronchial epithelial cell  Mock Uninfected
GSM4462364 Series9_NHBE_Mock_2 bronchial epithelial cell  Mock Uninfected
GSM4462365 Series9_NHBE_Mock_3 bronchial epithelial cell  Mock Uninfected
GSM4462366 Series9_NHBE_Mock_4 bronchial epithelial cell  Mock Uninfected
GSM4462367 Series9_NHBE_IAV_1 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4462368 Series9_NHBE_IAV_2 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4462369 Series9_NHBE_IAV_3 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4462370 Series9_NHBE_IAV_4 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus
GSM4462371 Series9_NHBE_IAVdNS1_1 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus Extra interventions
NS1 deleted
GSM4462372 Series9_NHBE_IAVdNS1_2 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus Extra interventions
NS1 deleted
GSM4462373 Series9_NHBE_IAVdNS1_3 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus Extra interventions
NS1 deleted
GSM4462374 Series9_NHBE_IAVdNS1_4 bronchial epithelial cell  12 hrs IAV (A/Puerto Rico/8/1934 (H1N1)) Influenza A virus Extra interventions
NS1 deleted
GSM4462375 Series9_NHBE_IFNB_4h_1 bronchial epithelial cell  4 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462376 Series9_NHBE_IFNB_4h_2 bronchial epithelial cell  4 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462377 Series9_NHBE_IFNB_6h_1 bronchial epithelial cell  6 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462378 Series9_NHBE_IFNB_6h_2 bronchial epithelial cell  6 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462379 Series9_NHBE_IFNB_12h_1 bronchial epithelial cell  12 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462380 Series9_NHBE_IFNB_12h_2 bronchial epithelial cell  12 hrs IFNB Uninfected Extra interventions
Interferon-stimulated
GSM4462413 Series15_HealthyLungBiopsy_1 lung  Healthy Uninfected
GSM4462414 Series15_HealthyLungBiopsy_2 lung  Healthy Uninfected
GSM4462415 Series15_COVID19Lung_1 lung  COVID-19 Severe acute respiratory syndrome-related coronavirus Data failed QC
pseudoaligned_reads is 96102 (low number of usable reads)
pct_pseudoaligned is 0.9% (low fraction of usable reads)
GSM4462416 Series15_COVID19Lung_2 lung  COVID-19 Severe acute respiratory syndrome-related coronavirus Data failed QC
pseudoaligned_reads is 1464206 (low number of usable reads)
pct_pseudoaligned is 15.4% (low fraction of usable reads)
GSM4486157 Series16_A549-ACE2_Mock_1 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4486158 Series16_A549-ACE2_Mock_2 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4486159 Series16_A549-ACE2_Mock_3 non-small cell lung adenocarcinoma cell line  [A-549 ] Mock Uninfected Extra interventions
overexpressed ACE2
GSM4486160 Series16_A549-ACE2_SARS-CoV-2_1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4486161 Series16_A549-ACE2_SARS-CoV-2_2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4486162 Series16_A549-ACE2_SARS-CoV-2_3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2
GSM4486163 Series16_A549-ACE2_SARS-CoV-2_Rux_1 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2 + Ruxolitinib treatment
GSM4486164 Series16_A549-ACE2_SARS-CoV-2_Rux_2 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2 + Ruxolitinib treatment
GSM4486165 Series16_A549-ACE2_SARS-CoV-2_Rux_3 non-small cell lung adenocarcinoma cell line  [A-549 ] SARS-CoV-2 (USA-WA1/2020) Severe acute respiratory syndrome-related coronavirus Extra interventions
overexpressed ACE2 + Ruxolitinib treatment