GEO DataSets

(Submitter supplied) The infrequently altered SARS-CoV-2 protein RNA dependent RNA polymerase (RdRp) is a promising target for T cell-targeting mRNA vaccines. We used single cell RNA sequencing (scRNA-seq) to define the transcriptional profile and TCR repertoire of CD8+ cells in mice immunized with a mRNA vaccine encoding SARS-CoV-2.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

2 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Gene expression analysis of RNA was performed using the commercially available NanoString® nCounter Immune Exhaustion gene expression panel (NanoString Technologies, Seattle, WA, USA). This panel contains 785 genes to elucidate mechanisms behind T cell, B cell and NK cell exhaustion in disease. Ribonucleic acid (RNA) was extracted from peripheral blood mononuclear cells (PBMCs) isolated from ME/CFS (n=14), long COVID (n=15), and healthy control (HC; n=18) participants. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33412

47 Samples

Download data: RCC, XLSX

(Submitter supplied) Memory T and B cells in lymphoid and mucosal tissues maintain long-term protection, though their generation following vaccination remains challenging to assess in humans. Here, we investigated immune memory generated to COVID-19 mRNA vaccines across blood, lymphoid organs, and lungs from 42 vaccinated organ donors aged 23-86, of whom 57% were previously infected with SARS-CoV-2. Using high-dimensional profiling, we reveal that Spike (S)-reactive memory T cells distribute in lymphoid organs and lungs, variably express tissue resident markers based on infection history, and exhibit site-specific compositions of effector and regulatory memory T cells. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL21697

82 Samples

Download data: TXT

(Submitter supplied) Type 2 diabetes (T2D) patients are more susceptible to severe respiratory viral infections, but the underlying mechanisms remain elusive. Here, we show that both COVID-19-infected T2D patients and influenza-infected T2D mice exhibit a defective Th1 response, which is an essential component of anti-viral immunity. This defect stems from intrinsic metabolic perturbations in CD4+T cells driven by hyperglycemia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL24676

9 Samples

Download data: CSV, MTX, TSV, XLSX

(Submitter supplied) Acute lung injury (ALI), ARDS and COVID-19 usually involve a “cytokine storm”. IGF1R (Insulin-like growth factor receptor 1) maintains lung homeostasis and is implicated in these pulmonary inflammatory diseases. In mice, widespread IGF1R deficiency was reported to counteract respiratory inflammation and alveolar damage after bleomycin (BLM)-induced ALI. To explore the molecular mechanisms mediated by Igf1r signaling after BLM challenge, we performed RNA-sequencing in lungs of IGF1R-deficient mice after BLM or saline (SAL) instillation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

12 Samples

Download data: TXT

(Submitter supplied) Using single-cell RNA-sequencing, we demonstrated that HBC subpopulations exhibit distinct cellular programs, with specific subpopulations differentially impacted by SARS-CoV-2. Assessment of differentially expressed genes implied impaired phagocytosis, a key function of both HBCs and microglia, in some subclusters. Leveraging previously validated models of microglial synaptic pruning, we showed that HBCs isolated from placentas of SARS-CoV-2 positive pregnancies can be transdifferentiated into microglia-like cells (HBC-iMGs), with impaired synaptic pruning behavior compared to HBC models from negative controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: MTX, TSV

(Submitter supplied) Clonal expansion is a hallmark of adaptive immunity, and appears to be driven by high antigen-specific receptor avidity as shown by research using murine in vivo models. In humans, however, the functionality of antigen-specific T cell clonotypes that are recruited into primary and recall immune responses remains surprisingly elusive. In this regard, the vaccination program during the SARS-CoV-2 pandemic represented a unique research opportunity by provision of highly standardized cohorts of healthy human individuals receiving immunizations against a previously unseen antigen. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV, H5

(Submitter supplied) Clonal expansion is a hallmark of adaptive immunity, and appears to be driven by high antigen-specific receptor avidity as shown by research using murine in vivo models. In humans, however, the functionality of antigen-specific T cell clonotypes that are recruited into primary and recall immune responses remains surprisingly elusive. In this regard, the vaccination program during the SARS-CoV-2 pandemic represented a unique research opportunity by provision of highly standardized cohorts of healthy human individuals receiving immunizations against a previously unseen antigen. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: CSV, H5

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

77 Samples

Download data: TAR

(Submitter supplied) Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to limited understanding of how pregnancy shapes and modulates immune responses. To gain insight into the roles of pregnancy in shaping the immune responses we collected peripheral blood mononuclear cells (PBMC) from 17 non-pregnant and 9 pregnant donors with various COVID severities and compared their immunological profiles.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

26 Samples

Download data: TAR

(Submitter supplied) Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to limited understanding of how pregnancy shapes and modulates immune responses. To gain insight into the roles of pregnancy in shaping the immune responses we collected peripheral blood mononuclear cells (PBMC) from 17 non-pregnant and 9 pregnant donors with various COVID severities and compared their immunological profiles.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

26 Samples

Download data: TAR

(Submitter supplied) Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to limited understanding of how pregnancy shapes and modulates immune responses. To gain insight into the roles of pregnancy in shaping the immune responses we collected peripheral blood mononuclear cells (PBMC) from 17 non-pregnant and 9 pregnant donors with various COVID severities and compared their immunological profiles.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

25 Samples

Download data: TAR, XLSX

(Submitter supplied) In this study, we stained liver tissues from COVID-19 cases with abnormal liver functions, and found viral proteins were detectable from dead or severe cases, but not from moderate patients. We then conducted spatial transcriptomics to analyze effects of SARS-COV-2 on livers.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

3 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Rapid emergence of antigenic distinct SARS-CoV-2 variants implies a greater risk of reinfection as viruses can escape neutralizing antibodies induced by vaccination or previous viral exposure. Disease severity during COVID-19 depends on many variables such as age-related comorbidities, host immune status and genetic variation. The host immune response during infection with SARS-CoV-2 may contribute to disease severity, which can range from asymptomatic to severe with fatal outcome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24973

4 Samples

Download data: CSV

(Submitter supplied) Cancer immunotherapy is gaining increasing attention. However, immune checkpoints are exploited by cancer cells to evade anti-tumor immunotherapy. Here, we knocked out NKG2A, an immune checkpoint expressed on natural killer (NK) cells, in human pluripotent stem cells (hPSCs) and differentiated these hPSCs into NK (PSC-NK) cells. We show that NKG2A knockout (KO) enhances the anti-tumor and anti-viral capabilities of PSC-NK cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: CSV

(Submitter supplied) Bats are tolerant to highly pathogenic viruses such as Marburg, Ebola, and Nipah, suggesting the presence of a unique immune tolerance toward viral infection. Here, we compared SARS-CoV-2 infection of human and bat (Rhinolophus ferrumequinum) pluripotent cells and fibroblasts. Since bat cells do not express an ACE2 receptor that allows virus infection, we transduced the human ACE2 receptor into the cells and found that transduced cells can be infected with SARS-CoV-2. more...

Organism:

Rhinolophus ferrumequinum; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32991 GPL24676

36 Samples

Download data: TXT

(Submitter supplied) In this study, we isolated RNA from the whole blood of 19 patients who developed myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) following acute SARS-CoV-2 infection. We also isolated RNA from the whole blood of 17 healthy controls (HCs). We analyzed the genes that had differential expression between patients with ME/CFS and HCs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

36 Samples

Download data: TSV

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection and vaccination induces T cell immunity as well as B cell responses in immunocompetent individuals. The mechanisms of anti-viral effect by CD4+ T cells as a part of T cell immunity are not fully understood. Here we used and analyzed the culture supernatant (SN) prepared from polyclonally stimulated human CD4+ T cells as a model of soluble mediator(s) from SARS-CoV-2-stimulated CD4+ T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX

(Submitter supplied) A key feature of RNA viruses, including SARS-CoV-2, is their high mutation rate, which allows them to develop resistance to vaccines and antiviral drugs targeting viral proteins. To overcome this downside, a strategy would be to target host factors, i.e. cell proteins required by the virus for its replication. However, it is still unclear whether cell responses induced by different SARS-CoV-2 variants are conserved and if the same core of host factors is exploited by different variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: TXT

(Submitter supplied) Paramyxoviruses (PMVs) exploit the host's translation machinery to enhance their replication. We found that the PMV matrix protein is crucial in this process, inhibiting host protein synthesis while boosting viral protein production. This occurs through interactions with the core exon-junction complex (cEJC), a key player in mRNA biogenesis. Disruption of this interaction using siRNA led to increased viral replication but did not affect other viruses like SARS-CoV-2. more...

Organism:

Human respirovirus 3; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL34775

21 Samples

Download data: XLSX