GEO DataSets

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

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

34 Samples

Download data: CSV

(Submitter supplied) SARS-CoV-2 induced hypercytokinemia and inflammation are critically associated with COVID-19 disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor, is currently being investigated in COVID-19 clinical trials. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

24 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 induced hypercytokinemia and inflammation are critically associated with COVID-19 disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor, is currently being investigated in COVID-19 clinical trials. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

10 Samples

Download data: CSV

(Submitter supplied) Patients often present with kidney injury in COVID-19. Although severe COVID-19 cases are treated with baricitinib, a JAK inhibitor, the effects of baricitinib on the kidneys in COVID-19 are unclear. The authors examined the pharmacological effects of baricitinib on kidney injury using an in vivo murine COVID-19 model.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) COVID-19 patients are generally asymptomatic during initial SARS-CoV-2 replication, but may suffer severe immunopathology after the virus has receded and blood monocytes have infiltrated the airways. In the bronchoalveolar lavage fluid from patients with severe COVID-19, lung-infiltrating monocytes expressed high mRNA levels encoding inflammatory mediators, including CXCL8and IL-1ß, and contained SARS-CoV-2transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

32 Samples

Download data: CSV, TXT

(Submitter supplied) The COVID-19 pandemic remains a global health crisis, yet, the immunopathological mechanisms driving the development of severe disease remain poorly defined. Here, we utilize a rhesus macaque (RM) model of SARS-CoV-2 infection to delineate perturbations in the innate immune system during acute infection using an integrated systems analysis. We found that SARS-CoV-2 initiated a rapid infiltration (two days post infection) of plasmacytoid dendritic cells into the lower airway, commensurate with IFNA production, natural killer cell activation, and induction of interferon-stimulated genes. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

101 Samples

Download data: TXT

(Submitter supplied) RNA-sequencing used to investigate the transcriptome response to Sars-cov-2 in the presence of IFN treatment

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

60 Samples

Download data: TXT

(Submitter supplied) Inflammation following SARS-CoV-2 infection is a hallmark of COVID-19 and predictive of morbidity and death. However, the inflammatory pathways contributing to host-defense vs immune-mediated pathology have not been fully elucidated. This duality is clearly seen with type-I interferons (IFN-I) which are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to site of infection, a key feature of severe COVID-19. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

240 Samples

Download data: CSV, H5

(Submitter supplied) To gain insights into the early immune dynamics of transcriptional changes during SARS-CoV-2 infection in airways, we performed longitudinal scRNA-Seq of the broncho-alveolar lavage (BAL) cells isolated from SARS-CoV-2 infected rhesus macaques. We found early induction of innate type-1 interferon responses with accumulation of a distinct macrophage population that possesses an interferon-driven innate anti-viral gene signature early during infection.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

18 Samples

Download data: MTX, TSV

(Submitter supplied) Older age is a key predictor of severe COVID-19. To gain insight into this relationship, especially with respect to immune responses, we utilized the rhesus macaque model of SARS-CoV-2 infection. Two cohorts of eight older (16-23 years) and eight younger (3-5 years) rhesus macaques were inoculated with SARS-CoV-2. Four animals per group were euthanized at 7- and 21-days post inoculation (dpi). Our time-resolved evaluation included viral RNA quantification, clinical observations, thoracic radiographs, single-cell transcriptomics, multiparameter flow cytometry, multiplex immunohistochemistry, cytokine detection, and lipidomics analysis. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29319

47 Samples

Download data: TAR

(Submitter supplied) The COVID-19 pandemic has led to extensive morbidity and mortality throughout the world. Clinical features that drive SARS-CoV-2 pathogenesis in humans include inflammation and thrombosis, but the mechanistic details that underlie these processes remain to be determined. In this study, we demonstrate endothelial disruption and vascular thrombosis in histopathologic sections of lungs from both humans and rhesus macaques infected with SARS-CoV-2. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

123 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 infection accounts for COVID-19 lung disease and other organ manifestations. Increasing evidence points towards an inflammatory cytokine network as the underlying driver of actual organ damage and severity of the clinical course. Here we show that SARS-CoV-2, like a broad spectrum of other viruses, evokes cellular senescence as a primary stress response in infected cells, among them respiratory epithelial cells, which is – indistinguishably from other forms of cellular senescence – characterized by typical morphological and cell-cycle arrest features, and accompanied by the massive secretion of largely pro-inflammatory cytokines, termed senescence-associated secretory phenotype (SASP).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28038 GPL20301

26 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 primarily replicates in mucosal sites, and more information is needed about immune responses in infected tissues. We used rhesus macaques to model protective primary immune responses in tissues during mild COVID-19. Viral RNA levels were highest on days 1-2 post-infection and fell precipitously thereafter. 18F-fluorodeoxyglucose (FDG)-avid lung abnormalities and interferon (IFN)-activated myeloid cells in the bronchoalveolar lavage (BAL) were found on days ∼3-4. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

14 Samples

Download data: MTX, TSV

(Submitter supplied) The majority of SARS-CoV-2 infections among healthy individuals result in asymptomatic to mild disease. However, the immunological mechanisms defining effective lung tissue protection from SARS-CoV-2 infection remain elusive. Unlike mice solely engrafted with human fetal lung xenograft (fLX), mice co-engrafted with fLX and a myeloid-enhanced human immune system (HNFL mice) are resistant to SARS-CoV-2 infection, severe inflammation, and histopathology. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30440

20 Samples

Download data: CSV

(Submitter supplied) The majority of SARS-CoV-2 infections among healthy individuals result in asymptomatic to mild disease. However, the immunological mechanisms defining effective lung tissue protection from SARS-CoV-2 infection remain elusive. Unlike mice solely engrafted with human fetal lung xenograft (fLX), mice co-engrafted with fLX and a myeloid-enhanced human immune system (HNFL mice) are resistant to SARS-CoV-2 infection, severe inflammation, and histopathology. more...

Organism:

Homo sapiens; Mus musculus; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30391

12 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

Platform:

GPL24676

45 Samples

Download data: H5

(Submitter supplied) Dexamethasone is the standard of care for critically ill patients with COVID-19, but its immunological effects in this setting and the mechanisms by which it decreases mortality are not understood. We performed bulk and single-cell RNA sequencing of the lower respiratory tract and blood, and plasma cytokine profiling to study the effect of dexamethasone on systemic and pulmonary immune cells. We find signatures of decreased viral injury, antigen presentation, and T cell recruitment in patients treated with dexamethasone. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

21 Samples

Download data: CSV

(Submitter supplied) Dexamethasone is the standard of care for critically ill patients with COVID-19, but its immunological effects in this setting and the mechanisms by which it decreases mortality are not understood. We performed bulk and single-cell RNA sequencing of the lower respiratory tract and blood, and plasma cytokine profiling to study the effect of dexamethasone on systemic and pulmonary immune cells. We find signatures of decreased viral injury, antigen presentation, and T cell recruitment in patients treated with dexamethasone. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: H5

(Submitter supplied) SARS-CoV-2 induces severe organ damage not only in the lung but also in the liver, heart, kidney, and intestine. It is known that COVID-19 severity correlates with liver dysfunction, but few studies have investigated the liver pathophysiology in COVID-19 patients. Here, we elucidated liver pathophysiology in COVID-19 patients using organs-on-a-chip technology and clinical analyses. First, we developed liver-on-a-chip (LoC) which recapitulating hepatic functions around the intrahepatic bile duct and blood vessel. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT