GEO DataSets

(Submitter supplied) The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and have been extensively described for well-characterized viruses. However, the extent to which viral RNA genomes contain functional structural elements – unable to be detected by sequence alone – that nonetheless are critical to viral fitness is largely unknown. more...

Organism:

dengue virus type 1; dengue virus type 3; dengue virus type 2; dengue virus type 4

Type:

Other

4 related Platforms

12 Samples

Download data: SHAPE, TXT

(Submitter supplied) Dengue virus (DENV) and Zika virus (ZIKV) are single-stranded (+)-sense RNA viruses that infect humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. more...

Organism:

dengue virus type 1; Zika virus

Type:

Other

Platforms:

GPL24217 GPL24221

26 Samples

Download data: CSV

(Submitter supplied) CEM.NKR.DC-SIGN cells were infected in vitro with DENV1 (strain WestPac74) for 18 hours, after which either total viable cells or viable cells expressing surface DENV1 NS1 were isolated by flow cytometric sorting. Sorted cells were processed for scRNAseq analysis using either a standard Oligo(dT) primer, or an Oligo(dT) primer supplemented with a DENV-specific RT primer

Organism:

Dengue virus 1 Nauru/West Pac/1974; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28282 GPL24676

4 Samples

Download data: MTX, TSV

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

Organism:

Homo sapiens; Dengue virus 1 Nauru/West Pac/1974; Dengue virus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28282 GPL24676 GPL28283

7 Samples

Download data: MTX, TSV

(Submitter supplied) Dengue and Zika are closely related members of the Flaviviridae family of positive, single-stranded RNA viruses and are of global clinical importance. These viruses utilize an 11kb RNA genome for translation and replication, and much remains to be learnt about how the entire genome folds to enable virus function. Here, we performed high throughput RNA secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains within their virus particles. more...

Organism:

Homo sapiens; dengue virus type 4; Zika virus; dengue virus type 1; dengue virus type 3; dengue virus type 2

Type:

Other

6 related Platforms

87 Samples

Download data: TXT

(Submitter supplied) Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. more...

Organism:

dengue virus type 1; dengue virus type 3; St. Louis encephalitis virus; Yellow fever virus; Guaroa virus; Aedes aegypti; Flaviviridae; Chikungunya virus; Rio Mamore hantavirus; Mucambo virus; Cacipacore virus; Iguape virus; Aedes albopictus; Togaviridae; Flavivirus; dengue virus type 2; Rhabdoviridae; Piry virus; Ilheus virus; Bussuquara virus; Rocio virus; Homo sapiens; Viruses; dengue virus type 4; West Nile virus; Dengue virus; Mayaro virus; Chlorocebus sabaeus; Zika virus; Oropouche virus

Type:

Expression profiling by array

Platforms:

GPL21870 GPL21871

87 Samples

Download data: GPR

(Submitter supplied) Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. more...

Organism:

dengue virus type 1; dengue virus type 3; Viruses; dengue virus type 4; Zika virus; dengue virus type 2; Aedes albopictus; Chikungunya virus

Type:

Expression profiling by array

Platform:

GPL21871

7 Samples

Download data: GPR

(Submitter supplied) Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. more...

Organism:

Flaviviridae; dengue virus type 3; Mucambo virus; Guaroa virus; Oropouche virus; Aedes albopictus; dengue virus type 2; Yellow fever virus; Piry virus; Chikungunya virus; Rio Mamore hantavirus; Cacipacore virus; Iguape virus; Aedes aegypti; Homo sapiens; Flavivirus; dengue virus type 4; Rhabdoviridae; Ilheus virus; Chlorocebus sabaeus; Bussuquara virus; Rocio virus; Viruses; Togaviridae; dengue virus type 1; St. Louis encephalitis virus; West Nile virus; Dengue virus; Mayaro virus

Type:

Expression profiling by array

Platform:

GPL21870

80 Samples

Download data: GPR

(Submitter supplied) Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. more...

Organism:

dengue virus type 2; dengue virus type 4; Dengue virus; dengue virus type 1; dengue virus type 3

Type:

Other

Platform:

GPL11294

12 Samples

Download data

(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; Monkeypox virus; dengue virus type 4; West Nile virus; Rift Valley fever virus; Chikungunya virus; Human poliovirus sp.; Hepacivirus hominis; Orthohantavirus seoulense; Orthohantavirus sinnombreense; Eastern equine encephalitis virus; Dengue virus; synthetic construct; Mammarenavirus lassaense; Orthohantavirus dobravaense; Orthohantavirus puumalaense; 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

Type:

Other

Platform:

GPL18370

64 Samples

Download data: PAIR

(Submitter supplied) The development of rapid and sensitive assays capable of detecting a wide range of infectious agents is critical for the effective diagnosis of diseases that have multiple etiologies. In recent years, many microarray-based diagnostics have been developed to identify viruses present in clinical specimens in a highly parallel fashion. Unfortunately, the rate of development of algorithms to interpret data generated from such platforms has not been commensurate. more...

Organism:

Flaviviridae; Arenaviridae; unidentified; Peribunyaviridae; Mammarenavirus juninense; Mammarenavirus choriomeningitidis; Mammarenavirus guanaritoense; Mammarenavirus lassaense; Mammarenavirus machupoense; Mammarenavirus praomyidis; Orthohantavirus puumalaense; dengue virus type 4; La Crosse virus; Rift Valley fever virus; Toscana virus; Kyasanur Forest disease virus; Orthohantavirus seoulense; dengue virus type 1; dengue virus type 3; Ebola virus - Gabon (1994-1997); Sudan ebolavirus; Ngari virus; Mammarenavirus amapariense; Mammarenavirus mopeiaense; Mammarenavirus tacaribeense; Orthohantavirus hantanense; Orthonairovirus haemorrhagiae; dengue virus type 2; Yellow fever virus; Filoviridae; Omsk hemorrhagic fever virus; California encephalitis virus; Rocio virus; Zaire ebolavirus; Reston ebolavirus; Lake Victoria marburgvirus - Angola2005; Mammarenavirus brazilense; Mammarenavirus ippyense

Type:

Other

Platform:

GPL10345

110 Samples

Download data: GPR

(Submitter supplied) This series includes microarrays from 36 patient samples and 2 cell-culture controls, used to optimize and validate the pathogen detection microarray (Wong, et. al. 2007) Keywords: viral pathogen detection

Organism:

dengue virus type 1; Viruses; Severe acute respiratory syndrome-related coronavirus

Type:

Expression profiling by array

Platform:

GPL5159

40 Samples

Download data: TXT

(Submitter supplied) RNA extraction Total RNA from cell culture supernatant of viruses from the different serotypes obtained from infected cells and from mosquitoes collected and frozen in the field was obtained using Trizol LS (GIBCO BRL, Gaithersburg, Md.) according to the manufacturer’s recommendations. Total RNA from acute-phase plasma collected from patients in the epidemiologic surveillance program by the Secretaria de Salud Oaxaca, Mexico during 2000- 2001 and 2004-2006 was also obtained by using the Viral Nucleic Acid Extraction Kit from Real Genomics (Real Biotech Corporation). more...

Organism:

dengue virus type 1; dengue virus type 2; dengue virus type 3; dengue virus type 4

1 Series

12 Samples

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