GEO DataSets

(Submitter supplied) We performed single-cell RNA sequencing on human bronchial epithelial cells infected with SARS-CoV-2. Results revealed a detailed characterization of genes, cell types, and cell state changes asociated with SARS-CoV-2 infection in the human airway.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: H5AD, MTX, TSV

(Submitter supplied) We performed RNAseq analysis on primary human airway epithelial cultures either mock infected (PBS) or infected with SARS-CoV-2. Transcriptional profiling studies found that infected pHAE cells had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8, and identified NF-κB and ATF4 as key drivers of this pro-inflammatory cytokine response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), a global pandemic characterized by respiratory illness and an exaggerated immune response. Age (>60 years) is a significant risk factor for developing severe COVID-19. However, the underlying mechanisms of how aging impacts SARS-CoV-2 infection and the host response are largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial 5 infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29320 GPL24676

10 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL16791

35 Samples

Download data: H5

(Submitter supplied) Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders including severe pneumonia. To develop a therapeutic drug for COVID-19, a model that can reproduce the viral life cycle and can evaluate the drug efficacy of anti-viral drugs is essential. In this study, we established a method to generate human bronchial organoids (hBO) from commercially available cryopreserved primary human bronchial epithelial cells (hBEpC) and examined whether they could be used as a model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

18 Samples

Download data: CSV

(Submitter supplied) Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, balancing virus control and immune-mediated pathology and have been successfully employed for the treatment of viral diseases. In humans, there are twelve IFN-alpha (α) subtypes, which activate downstream signalling cascades and result in a distinct pattern of immune responses and differential antiviral responses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

60 Samples

Download data: XLSX

(Submitter supplied) Single Cell Sequencing of SARS-CoV2 Infected Human Nasal Epithelial Cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: MTX, TSV, XLSX

(Submitter supplied) We have collected nasal cell swab samples from SARS-CoV-2 infected confirmed COVID-19 patients. Both virus and host RNA were extracted and sequenced by RNA-seq. We mapped and assembled virus sequences and in this study transcriptional profile of host due to virus infection.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) To test whether airway epithelial and immune cells in patients with severe SARS-CoV-2 pneumonia exhibit specific gene expression signatures (namely interferon-response signature) we have performed bronchoscopy on intubated patients with severe SARS-CoV-2 pneumonia and obtained bronchial brushings.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27644 GPL29811

9 Samples

Download data: H5

(Submitter supplied) Purpose: Numerous viruses manipulate the host translation machinery and specifically block host mRNA translation. The goal of this study is to define the translational landscape of SARS-CoV-2 and SARS-CoV-2 infected cells using a combination of RNA-seq and ribo-seq approches, the latter being a powerful proxy for protein-level changes. Methods: Vero E6 and primary human bronchial epithelial cells were infected with SARS-CoV-2 at varying multiplicities of infection and followed throughout early and late phases of infection. more...

Organism:

Chlorocebus sabaeus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL11154 GPL28836

156 Samples

Download data: TXT

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air-liquid interface culture system which was characterized by confocal-, electron-microscopy and single cell mRNA expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: TSV

(Submitter supplied) Bulk RNA sequencing was performed on control and SARS-CoV-2 infected 2D bronchioalveolar-like and small airway cultures Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: CSV

(Submitter supplied) mRNA expression in human bronchial epithelial cells unstimulated was compared with mRNA expression of cells stimulated with poly (I:C) (viral mimic) and poly (I:C) in combination with imiquimod (TLR7 agonist; Treatment). The aim was to assess the effect of imiquimod treatment on poly (I:C)-dependent changes in bronchial epithelium from asthmatics.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18649

9 Samples

Download data: RCC

(Submitter supplied) Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High-throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a pathogenic mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) Gene expression profile of human Nasal Epithelial Cells infected with SARS-CoV-2 and a 382-nt deletion strain, for the indicated time periods

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

21 Samples

Download data: TXT

(Submitter supplied) Airway epithelial brushings were obtained for microarray analysis by research bronchoscopy in 62 subjects with mild-to-moderate asthma not on inhaled steroids and 43 healthy controls. Asthma subjects were stratified into 2 subgroups, Th2 high and Th2 low asthma, based on their expression of a three-gene signature of Type 2 inflammation: POSTN, SERPINB2, and CLCA1.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16311

105 Samples

Download data: CEL

(Submitter supplied) Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection causes an immune-mediated disease. We have recently shown that SARS-CoV-induced epithelial Calu-3 cytokines could exacerbate and dampen host inflammatory and T cell responses, respectively, through modulating the functions of macrophages and dendritic cells, thereby suggesting that not only are lung epithelial cells the primary cells of SARS-CoV infection, but they also involve in initiating and orchestrating the host innate and adaptive immunity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

27 Samples

Download data: CEL

(Submitter supplied) Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We sought to further our understanding of the relationship between brain tropism, neuro-inflammation and host immune response in acute COVID-19 cases. 3 brain regions (dorsolateral prefrontal cortex, medulla oblongata and choroid plexus) from 5 patients with severe COVID-19 and 4 controls were examined. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

36 Samples

Download data: CSV

(Submitter supplied) To study the effect of cigarette smoke exposure on Sars-Cov2 infection, we directly exposed mucociliary air-liquid interface (ALI) cultures derived from primary human nonsmoker airway basal stem cells (ABSCs) to short term cigarette smoke and infected them with live SARS-CoV-2. We set out to examine the underlying mechanisms governing the increased susceptibility of cigarette smoke exposed ALI cultures to SARS-CoV-2 infection by usingle cell profiling of the cultures, which showed that interferon response genes were induced in SARS-CoV-2 infected airway epithelial cells in ALI cultures but smoking exposure together with SARS-CoV-2 infection reduced the interferon response.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TSV