GEO DataSets

(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) In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. more...

Organism:

Zea mays

Type:

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

Platform:

GPL9361

5 Samples

Download data: TXT

(Submitter supplied) Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9147 GPL9316

62 Samples

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(Submitter supplied) To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from root apices (RoApx), shoot apices (ShApx), developing inflorescence (Infl) and mature leaf (Leaf). These tissues were chosen because they are expected to be rich in small RNAs and display different patterns of small RNA expression. The RoApx, ShApx, and Infl samples are expected to be enriched for meristematic tissues each of which have different fates. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9388

12 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL8587

2 Samples

Download data: FNA, QUAL

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

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL17701 GPL15632

6 Samples

Download data: TXT

(Submitter supplied) We aimed to identify targets of miRNAs during wheat grain development by using degradome sequencing approach. Two degradome libraries were constructed from wheat grains.

Organism:

Triticum aestivum

Type:

Other

Platform:

GPL15632

2 Samples

Download data: TXT

(Submitter supplied) We aimed to identify differentially expressed miRNAs during wheat grain development by using high-throughput sequencing approach. Four small RNA libraries were constructed from wheat grains collected at 7, 14, 21 and 28 days post anthesis (DPA). A total of 165 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

4 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

28 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

24 Samples

Download data: TXT

(Submitter supplied) Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platforms:

GPL3777 GPL3776

5 Samples

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(Submitter supplied) An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10267

4 Samples

Download data: TXT

(Submitter supplied) Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. more...

Organism:

Cucurbita pepo; Lagenaria siceraria; Cucurbita moschata; Citrullus lanatus

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: TXT

(Submitter supplied) MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9147

1 Sample

Download data: TXT

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL9147

6 Samples

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(Submitter supplied) microRNAs (miRNAs) are a class of small silencing RNAs that have regulatory roles in gene expression. miRNAs interact with Argonaute (AGO) proteins to form effector complexes that can cleave target mRNAs or repress their translation. Rice encodes four AGO1 homologs (AGO1a, AGO1b, AGO1c, and AGO1d). We used an RNAi approach to knock down the four AGO1s. The RNAi lines displayed pleiotropic developmental phenotypes and had increased accumulation of miRNA targets, suggesting the involvement of AGO1s in the miRNA pathway. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

4 Samples

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(Submitter supplied) miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9147

2 Samples

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(Submitter supplied) miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. more...

Organism:

Arabidopsis thaliana; Oryza sativa; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

33 Samples

Download data: TXT

(Submitter supplied) Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for traits of agronomic importance like male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, play an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein which acts as a cofactor of MSP1 in the same regulatory pathway. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL13160

54 Samples

Download data: TXT