GEO DataSets

(Submitter supplied) In this study colorectal cancer (CRC) patient-derived cancer-associated fibroblasts (CAFs) and primary monocytes or macrophages were co-cultured in 2D set-up and single-cell transcriptomics was employed to analyze the phenotypic and functional changes of the myeloid cells and CAFs upon their interaction. The results showed that CAFs instruct monocytes to gain a tumor-associated macropages (TAM)-like cells phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: MTX, TSV

(Submitter supplied) Efforts to identify ccRNA by sequencing by gibson circularization after template-switching 5' RACE using a cRNA-end specific primer and subsequent sequencing by Illumina miSeq. Sequencing of wild-type A/WSN/1933 and a variant bearing the mutation T677A in the PB1 subunit.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

6 Samples

Download data: CSV

(Submitter supplied) Influenza A virus encodes promoters in both the sense and antisense orientations. These support the generation of new genomes, antigenomes, and mRNA transcripts. Characterization of the influenza promoters using minimal replication assays—transfections with viral polymerase, nucleoprotein, and a genomic template—defined their sequence as 13nt at the 5’ end of the viral genomic RNA (U13) and 12nt at the 3’ end (U12).Other than a single position the U12 and U13 sequences are identical between all eight RNA molecules that comprise the segmented influenza genome.Nevertheless, each segment can exhibit different transcriptional dynamics despite possessing identical promoters.Minimal replication assays lack the influenza protein NS2, which can modulate transcription and replication differentially between influenza segments.This suggests that NS2 expression may redefine the influenza A virus promoter.In this work we assess how internal regions of sequence in two genomic segments, HA and PB1, may contribute to NS2-dependent replication as well as map such interactions down to individual nucleotides in PB1. more...

Organism:

Influenza A virus (A/WSN/1933(H1N1))

Type:

Other

Platform:

GPL32752

30 Samples

Download data: TSV

(Submitter supplied) Pro-inflammatory autoantigen-specific CD4+ T helper (auto-Th) cells are central orchestrators of autoimmune diseases (AIDs). We aimed to characterize these cells in human AIDs with defined autoantigens by combining human leukocyte antigen (HLA)-tetramer-based and activation-based multidimensional ex vivo analyses. In aquaporin4-antibody-positive neuromyelitis optica spectrum disorder (AQP4-NMOSD) patients, auto-Th cells expressed CD154, but proliferative capacity and pro-inflammatory cytokines were strongly reduced. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

928 Samples

Download data: CSV

(Submitter supplied) Peripheral viral infection disrupts oligodendrocyte homeostasis such that endogenous remyelination may be affected. Here, we demonstrate that influenza A virus infection perpetuated a demyelination- and disease-associated oligodendrocyte (OL) phenotype following cuprizone-induced demyelination that resulted in delayed OL maturation and remyelination in the prefrontal cortex. Furthermore, we assessed cellular metabolism ex-vivo, and found that infection altered brain OL and microglia metabolism in a manner that opposed the metabolic profile induced by remyelination. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

12 Samples

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

(Submitter supplied) Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29847

22 Samples

Download data: XLSX

(Submitter supplied) Using gene expression data we developed a predictive signture to discriminate between typical bacterial, atyipcal bacterial, and viral pnuemonia in murine samples and validated it against open source human datasets.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

126 Samples

Download data: CEL

(Submitter supplied) To understand how different stimulation conditions impacted the maturation of B cells and formation of plasma cells in an ex vivo organoid culture, we preformed 10X single-cell RNA-seq comparing the CD19+ B cells and CD138+ plasma cells at different time points during the organoid culture. Three stimulation conditions were used including H1N1 influenza antigen alone, R848, H1N1 in combination with the TLR7 agonist R848. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The circulation of seasonal influenza A viruses (IAVs) in humans relies on effective evasion and subversion of the host immune response. While the evolution of seasonal H1N1 and H3N2 viruses to avoid humoral immunity is well characterized, relatively little is known about the evolution of innate immune antagonism phenotypes in these viruses. Numerous studies have established that only a small subset of infected cells are responsible for initiating the type I and type III interferon (IFN) response during IAV infection, emphasizing the importance of single cell studies to accurately characterize the IFN response during infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: MTX, TSV

(Submitter supplied) Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacts human health beyond acute infection. Myalgia and fatigue represent two of the most prevalent symptoms in post-COVID-19 syndrome. To determine the mechanisms underlying prolonged muscle symptoms, we characterized longitudinal histopathological and transcriptional changes of skeletal muscle after acute respiratory SARS-CoV-2 infection in a COVID-19 hamster model and compared them with respiratory influenza A virus (IAV) infection. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33389

21 Samples

Download data: TXT

(Submitter supplied) The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission, but the cellular composition at homeostasis, during infection, and during a memory response are poorly understood. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza A virus (IAV) infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL30172

42 Samples

Download data: CSV, H5

(Submitter supplied) The pig is a natural host for influenza viruses and integrally involved in virus evolution through interspecies transmissions between humans and swine. We employed scRNA-seq and flow cytometry to characterize the major leucocyte subsets in bronchoalveolar lavage (BAL), twenty-one days after H1N1pdm09 infection or respiratory immunization with an adenoviral vector vaccine expressing haemagglutinin and nucleoprotein with or without IL-1β. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

12 Samples

Download data: H5

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) Appropriate lung repair responses are essential to restore functional integrity and prevent severe disease phenotypes after injury. While macrophages are thought to contribute to repair, whether distinct subsets occupy particular niches and assume dedicated tasks to mediate host recovery post- injury remains unknown. Using an in vivo model of influenza A virus (IAV) infection in combination with single-cell and spatial transcriptomic analyses, bone marrow chimeras and monocyte fate-mapping, we found the transitional appearance of Ccr2-dependent monocyte-derived Ly6G+ macrophages (Ly6G Macs) after viral clearance. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) Current flu vaccine induces strong response to plastic and higly variable hemagglutinin (HA) head. However, response to conserved epitopes in HA elicited by current vaccine or infection is very limited. We hypothesized that change the relative "molarity" of immunodominant epitopes and conserved domain might increase response to conserved domains. Therfore, we made a library with the most ommunodominant domian Sb site randomized and tested its efficacy in vivo. more...

Organism:

Influenza A virus (A/Puerto Rico/8/1934(H1N1))

Type:

Other

Platform:

GPL30927

2 Samples

Download data: XLSX

(Submitter supplied) Influenza A virus (IAV) infection can cause the often-lethal acute respiratory distress syndrome (ARDS) of the lung. Concomitantly, acute kidney injury (AKI) is frequently noticed during IAV infection, correlating with an increased mortality. The aim of this study was to elucidate the interaction of IAV with human kidney cells and, thereby, to assess the mechanisms underlying IAV-mediated AKI. We demonstrate productive replication of low and highly pathogenic IAV strains on primary and immortalized nephron cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TSV, XLSX

(Submitter supplied) All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at air-liquid interface (ALI). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

26 Samples

Download data: CSV

(Submitter supplied) we performed transcriptomic analysis in A549 cells and demonstrated a reduced proinflammatory response but increased host tolerance upon H1N1 virus infection and mannose therapy, providing further evidence for the beneficial role of mannose in immunometabolism.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) This study explored the regulatory effect of D-mannose on host immunometabolic responses after viral infection. The results showed that D-mannose can compete with glucose for transporters and hexokinase, inhibiting glycolysis, reducing mitochondrial reactive oxygen species and succinate-induced HIF-1α, thereby reducing virus-induced inflammatory cytokine production. Even with delayed combinatorial treatment of D-mannose and antiviral monotherapy after viral infection, a synergistic effect was still observed in mouse models. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: XLSX

(Submitter supplied) Seasonal infection rates of individual viruses are influenced by synergistic or inhibitory interactions between coincident viruses. Endemic patterns of SARS-CoV-2 and influenza infection overlap seasonally in the Northern hemisphere and may be similarly influenced. We explored the immunopathologic basis of SARS-CoV-2 and influenza A (H1N1) interactions in Syrian hamsters. H1N1 given 48 hours prior to SARS-CoV-2 profoundly mitigated weight loss and lung pathology compared to SARS-CoV-2 infection alone. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28997

22 Samples

Download data: TXT