GEO DataSets

(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) 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) Objective: To evaluate the effect of short-term type I IFN treatment on the latent viral reservoir in SIV-infected rhesus macaques on ART; Methods: We infected twelve RMs intrarectally with 10,000 TCID of SIVmac239. After 6 weeks of infection, all RMs started a three-class, four-drug ART regimen. Once viral loads were consistently undetectable, six animals were administered 1 dose of pegylated IFN-α2a per week for 4 weeks with each weekly intramuscular application being 6 µg/kg.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23804

35 Samples

Download data: TXT

(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) 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) 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) Pathogenic HIV/SIV infection of humans and rhesus macaques (RMs) induces persistently high production of type-I interferon (IFN-I) which is thought to contribute to disease progression. To elucidate the specific role of IFN in SIV pathogenesis, 12 RMs were treated prior to i.v. SIVmac239 infection with a high or a low dose of an antibody (AGS-009) that neutralizes most IFN subtypes, and compared with six mock-infused, SIV-infected controls. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

107 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 has caused a historic pandemic of respiratory disease (COVID-19) and current evidence suggests severe disease is associated with dysregulated immunity within the respiratory tract1,2. However, the innate immune mechanisms that mediate protection during COVID-19 are not well defined. Here we characterize a mouse model of SARS-CoV-2 infection and find that early CCR2-dependent infiltration of monocytes restricts viral burden in the lung. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(Submitter supplied) We investigared the gene expression response of K18-ACE2 mices to Sars-Cov-2 infection. We compared gene expression profiles of control and infected mices at different time points as well as the infection from the Wuhan and Delta strains

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 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) RNA-seq was used to profile gene expression changes in human tracheobronchial epithelial (HTBE) and A549 cells following type I interferon treatment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 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) We retrospectively analysed the expression of 579 immunological genes in 60 COVID-19 subjects (SARS +ve) and 59 COVID-negative (SARS -ve) subjects using the NanoString nCounter (Immunology panel), a technology based on multiplexed single-molecule counting. Biobanked Human peripheral blood mononuclear cells (PBMCs) samples underwent Nucleic Acid extraction and digital detection of mRNA to evaluate changes in antiviral gene expression between SARS -ve controls and patients with mild (SARS +ve Mild) and moderate/severe (SARS +ve Mod/Sev) disease.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33240

119 Samples

Download data: RCC

(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) Within the context of the DUB module in the SAGA complex, USP22 is involved in transcriptional elongation through the regulation of H2AK119ub1 and H2BK120ub1. However, up till now, the spectrum of USP22-regulated target genes largely remains unclear, partially due to organism-, cell- and context-dependent redundancy in alternative DUBs that might compensate for loss of USP22. To understand which genes are regulated by USP22, we profiled USP22-dependent changes in gene expression in the human intestinal epithelial cell (hIEC) line HT-29.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

9 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) Purpose of experiment was to perform transcriptomic analysis on C57Bl/6 mice infected with different doses of SARS CoV MA15 at 4 different days post infection.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

92 Samples

Download data: TXT

(Submitter supplied) We infected Calu3 cells (derived from human lung epithelium) with SARS-CoV-2 for 24 and 48 hours. Calu3 cells were also treated with the STING agonist diABZI for 6 and 12 hours. Finally, heterozygous K18-hACE c57BL/6J mice were treated with diABZI for 6 and 12 hours and lung tissue was harvested for sequencing.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

40 Samples

Download data: CSV, SF