GEO DataSets

(Submitter supplied) All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. more...

Organism:

Locusta migratoria

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9308

2 Samples

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

Organism:

Phytophthora sojae; Phytophthora ramorum; Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17597 GPL17596 GPL17598

4 Samples

Download data: GFF3

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...

Organism:

Phytophthora sojae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17598

1 Sample

Download data: GFF3

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...

Organism:

Phytophthora ramorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17597

1 Sample

Download data: GFF3

(Submitter supplied) Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nucleotides long. We present evidence that 25-nucleotide small RNAs are short-interfering RNAs that silence repetitive genetic elements. more...

Organism:

Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17596

2 Samples

Download data: GFF3

(Submitter supplied) We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon

Organism:

Trichoplax adhaerens; Nematostella vectensis; Monosiga brevicollis; Amphimedon queenslandica

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

17 Samples

Download data: TXT

(Submitter supplied) Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11221

6 Samples

Download data: XLSX

(Submitter supplied) DNA methylation is a widely conserved epigenetic modification that is established and maintained by the cooperative activity of DNA methyltransferases. While the complement of DNA methyltransferase genes can vary substantially between animal species, whole-genome methylation analyses have suggested that major features of animal methylomes are widely conserved. We have now used genome-scale bisulfite sequencing to analyze the methylome of the desert locust, Schistocerca gregaria, which represents an economically important pest with a high degree of phenotypic plasticity. more...

Organism:

Schistocerca gregaria

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16114

2 Samples

Download data: BEDGRAPH

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

Organism:

Citrullus lanatus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23842 GPL20225

15 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...

Organism:

Citrullus lanatus

Type:

Other

Platform:

GPL23842

1 Sample

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...

Organism:

Citrullus lanatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20225

14 Samples

Download data: TXT

(Submitter supplied) Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. more...

Organism:

Ornithorhynchus anatinus; Tachyglossus aculeatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11057 GPL11058

3 Samples

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(Submitter supplied) We performed extensive transcriptome analysis of the tiger pufferfish (Takifugu rubripes) using the next-generation sequencer SOLiD III, and profiled millions of small RNA sequences in somatic tissues and gonads, as well as identifying thousands of miRNAs. The number of miRNAs identified was the highest in fish species reported to date. We also report highly variable isomiR features.

Organism:

Takifugu rubripes

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19713

9 Samples

Download data: TXT

(Submitter supplied) Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9147 GPL9388

6 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL17021

4 Samples

Download data: TXT