GEO DataSets

(Submitter supplied) In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. more...

Organism:

Homo sapiens; Sindbis virus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL33716 GPL20301

26 Samples

Download data: BW, TXT

(Submitter supplied) In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. more...

Organism:

Homo sapiens; Sindbis virus

Type:

Other

Platform:

GPL33716

8 Samples

Download data: BW, TXT

(Submitter supplied) In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. more...

Organism:

Homo sapiens; Sindbis virus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33716 GPL20301

18 Samples

Download data: TXT

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

Organism:

Chikungunya virus; Homo sapiens; Dengue virus

Type:

Other

Platforms:

GPL33379 GPL33380

8 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) N6-methyladenosine (m6A), the most common internal RNA modification in eukaryotic mRNAs, is described to be abundantly present in the genomes of cytoplasmic-replicating RNA viruses. Yet, how the host nuclear m6A writer has access to the viral RNAs in the cytoplasm and what are the associated biological consequences remain unknown. Here, we comprehensively addressed these questions by combining antibody-dependent (m6A-seq) and antibody-independent (SELECT and nanopore direct RNA sequencing) methods on the cytoplasmic-replicating Chikungunya virus (CHIKV) RNA, and found no evidence of m6A modifications. more...

Organism:

Homo sapiens; Chikungunya virus

Type:

Other

Platform:

GPL33379

4 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) RNA viruses have developed elaborate strategies for 5’ capping and protection of their genomes. However, so far no 5’ RNA cap has been identified for Hepatitis C virus (HCV), which cause chronic infection, liver cirrhosis and cancer in humans4. Here, we demonstrate that the cellular metabolite flavin adenine dinucleotide (FAD) is used as noncanonical initiating nucleotide by the viral RNA-dependent RNA polymerase resulting in a 5’ FAD cap on the HCV RNA. more...

Organism:

Bovine viral diarrhea virus 1-NADL; Chikungunya virus; Homo sapiens; Bos taurus; Tick-borne encephalitis virus; Hepacivirus hominis

Type:

Other

4 related Platforms

168 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) on targeted locus in Sindbis genome to determine frequency changes of artificial microRNAs expressed by viruses after passaging in cancer and normal cells Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. Sequencing was done by SeqMatic on a MiSeq v3 platform generating 75bp reads. more...

Organism:

Sindbis virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23568

21 Samples

Download data: TXT

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

Organism:

Chikungunya virus; Bordetella pertussis; Plasmodium falciparum; Staphylococcus aureus; Onchocerca volvulus; Yellow fever virus; Streptococcus sp. 'group B'; Mycobacterium tuberculosis; Homo sapiens; Dengue virus; Human immunodeficiency virus; Respiratory syncytial virus; Zika virus

Type:

Protein profiling by protein array

Platform:

GPL29530

804 Samples

Download data

(Submitter supplied) Breastfeeding provides defense against infectious disease during early life. The mechanisms underlying this protection are complex but likely include the vast array of immune cells and components, such as immunoglobulins, in milk. Simply characterizing the concentrations of these bioactives, however, provides only limited information regarding their potential relationships with disease risk in the recipient infant. more...

Organism:

Streptococcus sp. 'group B'; Onchocerca volvulus; Dengue virus; Human immunodeficiency virus; Respiratory syncytial virus; Zika virus; Bordetella pertussis; Mycobacterium tuberculosis; Plasmodium falciparum; Homo sapiens; Staphylococcus aureus; Yellow fever virus; Chikungunya virus

Type:

Protein profiling by protein array

Platform:

GPL29530

402 Samples

Download data: TXT

(Submitter supplied) Breastfeeding provides defense against infectious disease during early life. The mechanisms underlying this protection are complex but likely include the vast array of immune cells and components, such as immunoglobulins, in milk. Simply characterizing the concentrations of these bioactives, however, provides only limited information regarding their potential relationships with disease risk in the recipient infant. more...

Organism:

Yellow fever virus; Chikungunya virus; Bordetella pertussis; Mycobacterium tuberculosis; Plasmodium falciparum; Homo sapiens; Respiratory syncytial virus; Staphylococcus aureus; Streptococcus sp. 'group B'; Onchocerca volvulus; Dengue virus; Human immunodeficiency virus; Zika virus

Type:

Protein profiling by protein array

Platform:

GPL29530

402 Samples

Download data: TXT

(Submitter supplied) Using photoactivatable ribonucleoside crosslinking and biotinylated Cp retrieval, multiple binding sites on viral gRNA where identified.

Organism:

Semliki Forest virus

Type:

Other

Platform:

GPL29026

6 Samples

Download data: XLSX

(Submitter supplied) Sindbis virus is a mutagenic ssRNA arbor virus. The structural genome component of this virus can be exchanged for any transgene of < 6kb in size. Here we sequence transgenic elements inserted to the virus. Our EGFP transgene was analyzed as a function of time during viral replication to quantify the mutagenic rate of the virus. Our nanobody transgene was analyzed to assess cDNA library complexity and identity.

Organism:

Sindbis virus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25880

22 Samples

Download data: CSV, FASTA, PY, TXT, XLSX

(Submitter supplied) The goal of this project was the analysis of virus variants resistant to β-D-N(4)-hydroxycytidine.

Organism:

Venezuelan equine encephalitis virus

Type:

Other

Platform:

GPL24256

13 Samples

Download data: PDF, XLSX

(Submitter supplied) Alphaviruses are arthropod-borne viruses that represent a significant threat to public health at a global level. While the formation of alphaviral nucleocapsid cores, consisting of cargo nucleic acid and the viral capsid protein, is an essential molecular process of infection, the precise interactions between the two partners are ill-defined. A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. more...

Organism:

Sindbis virus; Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL23568

5 Samples

Download data: XLSX

(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) We performed whole genome single nucleotide polymorphism (SNP) based analysis of all available Venezuelan equine encephalitis (VEE) virus antigenic complex genomes and developed a high resolution genome-wide SNP microarray. We used the SNP microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array and sequence based genotypes for previously sequenced strains, and genotyped unsequenced strains.

Organism:

Pixuna virus; Cabassou virus; Venezuelan equine encephalitis virus; Mucambo virus

Type:

SNP genotyping by SNP array

Platform:

GPL21646

141 Samples

Download data: PAIR

(Submitter supplied) The role of RNA silencing as a defense mechanism against viruses remains to be formerly established in mammalian somatic cells. Here, we determined the antiviral properties of human and Drosophila Dicer proteins in a heterologous setup. We expressed human Dicer (hDicer) in Drosophila, and Drosophila Dicer-2 in human cells, and measured the impact on the response to Sindbis virus (SINV) infection. In flies, hDicer presents a low processing activity, but partially rescues a Dcr2 null mutation in flies. more...

Organism:

Drosophila melanogaster; Homo sapiens; Sindbis virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19381 GPL19380

11 Samples

Download data: BED, TXT

(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