GEO DataSets

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

Organism:

Cymbidium ringspot virus; Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15026 GPL10313

6 Samples

Download data: FNA, QUAL

(Submitter supplied) We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation-based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. more...

Organism:

Cymbidium ringspot virus; Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15026

2 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation-based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. more...

Organism:

Cymbidium ringspot virus; Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10313

4 Samples

Download data: TXT

(Submitter supplied) RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. more...

Organism:

Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21356

29 Samples

Download data: TXT

(Submitter supplied) Viral suppressors of RNA silencing, VSRs, counteract the antiviral RNA silencing of host plants by sequestration of virus-derived siRNAs. A central question concerns whether and how VSRs associate cellular miRNAs and thus modulate plant gene expression during a viral infection. In this study we characterize the binding behaviour of the tombusviral p19 protein to miRNAs by performing an RNA-pull down experiment with bead-associated p19 protein from carnation italian ringspot virus. more...

Organism:

Nicotiana tabacum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23484

6 Samples

Download data: FA, TXT

(Submitter supplied) Both Southern rice black-streaked dwarf virus (SRBSDV) and Rice ragged stunt virus (RRSV) belong to the family Reoviridae, and synergistic infection of these two viruses commonly occurs in the field. This study revealed that both SRBSDV and RRSV affect the RNA interference (RNAi) pathway and form different virus-derived interfering RNA (vsiRNA) profiles in rice. Co-infection of rice by SRBSDV and RRSV up-regulated the expression of rice Dicer and DICER-like (DCL) proteins but down-regulated the expression of rice RNA-dependent RNA polymerases (RDRs), and the accumulation of vsiRNAs of either RBSDV or RRSV was decreased compared with that in singly infected plants. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

3 Samples

Download data: TXT

(Submitter supplied) Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus. more...

Organism:

Youcai mosaic virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9403

4 Samples

Download data: TXT

(Submitter supplied) In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. more...

Organism:

Botrytis cinerea; Botrytis paeoniae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL22004 GPL22005

3 Samples

Download data: TXT

(Submitter supplied) Small RNA libraries of 4 different mycovirus-infected and -free isogenic lines of A. fumigatus were constructed using Scriptminer adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified.

Organism:

Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18295

16 Samples

Download data: CSV

(Submitter supplied) Small RNA libraries of three different mycovirus-infected A. fumigatus isolates were constructed by using Illumina high definition adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified.

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18295

3 Samples

Download data: CSV

(Submitter supplied) We investigated the role of A. thaliana RDRs in the RNAi-mediated viral immunity by using a mutant of cucumber mosaic virus (CMV) that does not express the VSR protein 2b. CMV contains three positive-strand genomic RNAs and the 2b protein encoded by RNA2 is essential for infection by suppressing antiviral silencing initiated by either DCL4 or DCL2. Our results demonstrate an essential role for the amplification of viral siRNAs by either RDR1 or RDR6 in antiviral silencing. more...

Organism:

Arabidopsis thaliana; Cucumber mosaic virus (strain FNY)

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9951

6 Samples

Download data