GEO DataSets

(Submitter supplied) During the life cycle of Enterovirus 71 (EV71), N6-methyladenosine (m6A) modification has an important impact on viral replication and the cellular response to viral infection, but the effect of m6A modification on cellular RNAs and pathways during infection is still unknown. The purpose of this research was to investigate the role of m6A in regulating host cell inflammatory response and disease progression during EV71 infection. more...

Organism:

Enterovirus A71; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL33473 GPL24676

12 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) is a cell-intrinsic antiviral defense conserved in diverse organisms. However, the mechanism by which mammalian antiviral RNAi is regulated is largely unknown. Herein, we uncover that STUB1, an E3 ubiquitin ligase, interacts with and ubiquitinates AGO2, the core component of RNAi pathway, resulting in the degradation of AGO2 via ubiquitin-proteasome system. Additionally, STUB1 can induce the degradation of the other mammalian AGO proteins including AGO1, AGO3, and AGO4. more...

Organism:

Enterovirus A71; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30983

2 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) is an antiviral immunity conserved in diverse eukaryotes including mammals, while viruses encodes viral suppressors of RNAi (VSRs) as countermeasures. However, the physiological impact of RNAi on viral infection in mammals has not been fully assessed, and it also remains unknown whether antiviral RNAi can be therapeutically exploited. Here, we show that peptides designed to target enterovirus A71 (EV-A71)-encoded protein 3A, a well-characterized VSR, triggered an effective antiviral response. more...

Organism:

Enterovirus A71

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL30355

8 Samples

Download data: TXT

(Submitter supplied) The capability of the U.S. Food and Drug Administration Enteric Viruses tiling microarray (FDA-EVIR) was assessed for rapid molecular identification of human norovirus (NoV) and hepatitis A virus (HAV) extracted from artificially inoculated fresh produce. Two published viral extraction strategies, total RNA extraction or virus particle isolation, were employed to prepare the viral targets. We also assessed the amount of viral RNA extracted from celery by three commercially-available kits and how well that RNA performed on the FDA-EVIR. more...

Organism:

Allium fistulosum; Bacillus subtilis; unidentified adenovirus; Hepatovirus A; Astrovirus sp.; Rotavirus; Paslahepevirus balayani; Apium graveolens; Solanum lycopersicum; Coxsackievirus; Sapovirus; Norovirus

Type:

Expression profiling by genome tiling array

Platform:

GPL27751

17 Samples

Download data: CEL

(Submitter supplied) Viruses can disperse collectively using extracellular vesicles and other types of multi-virion structures. It has been hypothesized that, by increasing the cellular multiplicity of infection, this dispersal mode may favor cooperation among viral genomes. However, the spread of defective variants that function as social cheaters could also be promoted. To better understand the nature of virions present in vesicles, here we examine the genetic diversity harboured by vesicles of coxsackievirus B3 (CVB3), a model enterovirus. more...

Organism:

Coxsackievirus B3 (strain Nancy)

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL25992

7 Samples

Download data: XLSX

(Submitter supplied) Immunomodulatory mechanisms associated with clearance versus persistence of foot-and-mouth disease virus (FMDV) in micro-dissected compartments of the bovine nasopharynx were investigated using qRT-PCR and whole transcriptome microarray. Analysis of tissue samples obtained by laser capture microdissection (LCM) during transitional and persistent phases of infection demonstrated significant differences in transcriptome profiles of animals that cleared infection versus those that became persistently infected carriers. more...

Organism:

Bos taurus; Foot-and-mouth disease virus; Human adenovirus 5

Type:

Expression profiling by array

Platform:

GPL22061

32 Samples

Download data: GPR

(Submitter supplied) In this study the gene expression in cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells, next generation sequencing was performed, and the reads were subsequently mapped against the human and CVB2O genomes. more...

Organism:

Homo sapiens; Coxsackievirus B2 (strain Ohio-1)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20238

4 Samples

Download data: TXT

(Submitter supplied) Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features.  The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV.  The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms

Organism:

Foot-and-mouth disease virus

Type:

Other

Platform:

GPL22607

8 Samples

Download data: FASTA, GPR

(Submitter supplied) In order to investigate the mechanisms of persistent foot-and-mouth disease virus (FMDV) infection in cattle, transcriptome alterations associated with the FMDV carrier state were characterized using a bovine whole-transcriptome microarray. Eighteen cattle (8 vaccinated with a recombinant FMDV A vaccine, 10 non-vaccinated) were challenged with FMDV A24 Cruzeiro, and the gene expression profiles of nasopharyngeal tissues collected between 21 and 35 days after challenge were compared between 11 persistently infected carriers and 7 non-carriers. more...

Organism:

Foot-and-mouth disease virus; Human adenovirus 5; Bos taurus

Type:

Expression profiling by array

Platform:

GPL22061

40 Samples

Download data

(Submitter supplied) While RNA interference (RNAi) functions as a potent antiviral innate immune response in plants and invertebrates, mammalian somatic cells appear incapable of mounting an RNAi response and few small interfering RNAs (siRNAs) can be detected. To examine why siRNA production is inefficient, we have generated double knockout human cells lacking both Dicer and PKR. Using these cells, which tolerate dsRNA expression, we show that mutant forms of human Dicer lacking the amino-terminal helicase domain can process dsRNAs to produce high levels of siRNAs that are readily detectable by Northern blot and that can effectively and specifically inhibit the expression of cognate mRNAs. more...

Organism:

Human poliovirus 1 strain Sabin; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL20271

21 Samples

Download data: BED, FA

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

Organism:

Helicobacter pylori; Yersinia enterocolitica; Chlamydia trachomatis; Mycobacterium tuberculosis variant bovis; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Coxsackievirus B4; Coxsackievirus A20; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Proteus mirabilis; Streptococcus pyogenes; Mycobacterium gordonae; Trypanosoma cruzi; Caprine arthritis encephalitis virus; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Human rotavirus MP409; Paraburkholderia fungorum; Staphylococcus aureus A9635; Hepacivirus hominis; Escherichia coli; Shigella flexneri; Haemophilus influenzae; Staphylococcus aureus; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human betaherpesvirus 6; human gammaherpesvirus 4; Human T-cell leukemia virus type I; Coxsackievirus A9; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Betapolyomavirus macacae; Klebsiella pneumoniae; Porphyromonas gingivalis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human herpesvirus 4 strain B95-8; Human immunodeficiency virus 1; Human herpesvirus 4 type 1; Coxsackievirus B4 (strain E2)

Type:

Protein profiling by protein array

Platforms:

GPL19700 GPL19692 GPL19701

29 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Porphyromonas gingivalis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mycobacterium gordonae; Mus musculus; Human betaherpesvirus 6; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Human herpesvirus 4 type 1; Human endogenous retrovirus K; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Coxsackievirus A9; Coxsackievirus B4 (strain E2); Betapolyomavirus macacae; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Trypanosoma cruzi; Homo sapiens; Human herpesvirus 4 strain B95-8; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Helicobacter pylori; Shigella flexneri; Yersinia enterocolitica; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human T-cell leukemia virus type I; Coxsackievirus A20; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Staphylococcus aureus A9635

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Mycobacterium tuberculosis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human herpesvirus 4 strain B95-8; Human T-cell leukemia virus type I; Coxsackievirus A9; Prochlorococcus marinus str. MIT 9202; Coxsackievirus B4 (strain E2); Staphylococcus aureus A9635; Betapolyomavirus macacae; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mus musculus; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Trypanosoma cruzi; Human betaherpesvirus 6; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Helicobacter pylori; Proteus mirabilis; Yersinia enterocolitica; Porphyromonas gingivalis; Mycobacterium gordonae; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human herpesvirus 4 type 1; Coxsackievirus A20; Torque teno virus; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

(Submitter supplied) Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travelling, climate changes and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. For many of them, the disease symptoms are similar to each other, as well as to other more common diseases, making them difficult to diagnose. A rapid identification will help to decide about specific treatment and appropriate case management. more...

Organism:

dengue virus type 2; Yellow fever virus; Toscana virus; Usutu virus; Zaire ebolavirus; Cowpox virus; Orf virus; dengue virus type 1; dengue virus type 3; Japanese encephalitis virus; Tick-borne encephalitis virus; sandfly fever Sicilian virus; Marburgvirus; Sandfly fever Naples virus; Orthohantavirus hantanense; Orthonairovirus haemorrhagiae; Eastern equine encephalitis virus; Dengue virus; synthetic construct; Mammarenavirus lassaense; Orthohantavirus dobravaense; Orthohantavirus puumalaense; Monkeypox virus; dengue virus type 4; West Nile virus; Rift Valley fever virus; Chikungunya virus; Human poliovirus sp.; Hepacivirus hominis; Orthohantavirus seoulense; Orthohantavirus sinnombreense

Type:

Other

Platform:

GPL18370

64 Samples

Download data: PAIR

(Submitter supplied) We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

Organism:

Homo sapiens; hepatitis C virus genotype 1a; Poliovirus 1

Type:

Other

4 related Platforms

37 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs), including host miRNAs and viral miRNAs, play vital roles in regulating host-virus interactions. DNA viruses encode miRNAs that regulate the viral life cycle. However, it is generally believed that cytoplasmic RNA viruses do not encode miRNAs, owing to inaccessible cellular miRNA processing machinery. Here, we provide a comprehensive genome-wide analysis and identification of miRNAs that were derived from hepatitis A virus (HAV; Hu/China/H2/1982), which is a typical cytoplasmic RNA virus. more...

Organism:

Homo sapiens; Hepatovirus A

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18215 GPL11154

2 Samples

Download data: FA

(Submitter supplied) Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travelling, climate changes and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. For many of them, the disease symptoms are similar to each other, as well as to other more common diseases, making them difficult to diagnose. A rapid identification will help to decide about specific treatment and appropriate case management. more...

Organism:

Cowpox virus; Orf virus; Marburgvirus; Orthohantavirus dobravaense; Zaire ebolavirus; Hepacivirus hominis; Mammarenavirus lassaense; Monkeypox virus; West Nile virus; Yellow fever virus; Rift Valley fever virus; Toscana virus; sandfly fever Sicilian virus; Chikungunya virus; Human poliovirus sp.; Sandfly fever Naples virus; Orthohantavirus hantanense; Orthohantavirus seoulense; Orthohantavirus sinnombreense; Eastern equine encephalitis virus; dengue virus type 2; Dengue virus; synthetic construct; Usutu virus; Orthohantavirus puumalaense; Orthonairovirus haemorrhagiae

Type:

Other

Platform:

GPL17919

42 Samples

Download data: PAIR

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

Organism:

Viruses; West Nile virus; Chlorocebus aethiops; Homo sapiens; Human alphaherpesvirus 1; Zaire ebolavirus; SARS coronavirus Tor2; Lassa virus Josiah; Vesicular stomatitis Indiana virus; Human adenovirus E4; Echovirus E18; artificial sequences; Influenza A virus (A/Texas/36/1991(H1N1))

Type:

Expression profiling by array

Platforms:

GPL10319 GPL10320

40 Samples

Download data: TXT

(Submitter supplied) Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. more...

Organism:

Vesicular stomatitis Indiana virus; Echovirus E18; Influenza A virus (A/Texas/36/1991(H1N1)); Chlorocebus aethiops; Human alphaherpesvirus 1; Human adenovirus E4; Zaire ebolavirus; SARS coronavirus Tor2; Lassa virus Josiah; Viruses; West Nile virus

Type:

Expression profiling by array

Platform:

GPL10320

11 Samples

Download data: TXT

(Submitter supplied) Laboratory strain poliovirus was hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-polio probes was evaluated. Specificity of the probe design was determined. Keywords: control study: target detection and specificity

Organism:

Viruses; Enterovirus C

Type:

Expression profiling by array

Platform:

GPL6501

3 Samples

Download data: GPR