GEO DataSets

(Submitter supplied) Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. more...

Organism:

Tomato yellow leaf curl virus; Cymbidium ringspot virus; Pepper mild mottle virus; Melon necrotic spot virus; Potato virus X; Turnip mosaic virus; Cucumber mosaic virus; Tobacco rattle virus; Watermelon mosaic virus

Type:

Non-coding RNA profiling by high throughput sequencing

9 related Platforms

10 Samples

Download data: TXT

(Submitter supplied) In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14001

3 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:

GPL22005 GPL22004

3 Samples

Download data: TXT

(Submitter supplied) We have investigated short and small RNAs (sRNAs) that were bound to a biologically active hexahistidine-tagged Potato virus Y (PVY) HCPro suppressor of silencing, expressed from a heterologous virus vector in Nicotiana benthamiana plants, and purified under non-denaturing conditions. We found that RNAs in purified preparations were differentially enriched in sRNAs of 21 and to a much lesser extent of 22 nucleotides (nt) in length and of viral sequence (vsRNAs) when compared to those found in a control plant protein background bound to the nickel resin in the absence of HCPro, or in a purified alanine substitution HCPro mutant (HCPro mutB) control that lacked suppressor of silencing activity. more...

Organism:

Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17448

6 Samples

Download data: TXT

(Submitter supplied) RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of a 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma, and by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16nt). more...

Organism:

Staphylococcus aureus; synthetic construct; Salmonella enterica subsp. enterica serovar Typhimurium; Pseudomonas aeruginosa PA7; Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655; Legionella pneumophila

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

12 Samples

Download data: FA, PDF