Virus Expression Database
Submitted by Daniel Blanco Melo (Icahn School of Medicine at Mount Sina, USA) on Apr 20 2020
Platform: ngs – Illumina NextSeq 500 (Homo sapiens)
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.
| 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 QCpseudoaligned_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 QCpseudoaligned_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 |