GEO DataSets

(Submitter supplied) The small RNAs of Selaginella moellendorffii were sampled by direct pyrosequencing (454 Life Sciences). These data represent microRNAs, siRNAs, and other expressed small RNAs of ~18-~28 nts. in length. Keywords: Small RNA sequencing - high throughput

Organism:

Selaginella moellendorffii

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL5014

1 Sample

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(Submitter supplied) High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL3886

3 Samples

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(Submitter supplied) To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17793

30 Samples

Download data: TXT

(Submitter supplied) Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times. Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT". Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16754

10 Samples

Download data: TXT

(Submitter supplied) Endogenous 24nt short interfering RNAs (siRNAs) derived mostly from intergenic and repetitive genomic regions constitute a major class of endogenous small RNAs in Arabidopsis thaliana. Accumulation of A. thaliana 24nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21nt microRNAs (miRNAs) and 21-22nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. more...

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9391

6 Samples

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(Submitter supplied) Inflorescence stages 1 to 12 from mutants involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and siRNAs). Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

44 Samples

Download data: CEL, CHP, RPT

(Submitter supplied) MicroRNAs (miRNAs) regulate the expression of target mRNAs in plants and animals. Plant miRNA targets have been predicted based on their extensive and often conserved complementarity to the miRNAs, as well as from miRNA over-expression experiments; many of these target predictions have been confirmed by isolating the products of miRNA-directed cleavage. Here, we present a transcriptome-wide experimental method, called “degradome sequencing,” to directly detect cleaved miRNA targets without relying on predictions or over-expression. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL6684 GPL6666

4 Samples

Download data: FNA, 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) High-throughput sequencing of Arabidopsis thaliana endogenous small RNAs by 454 pyrosequencing. Keywords: high-throughput sequencing

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL3968

4 Samples

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(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) Deep sequencing of Arabidopsis thaliana small RNAs was conducted to reveal microRNAs (miRNAs) and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6-1.2 million unique sequence tags from each Pi-sufficient or -deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778 and miR827 was induced, whereas the expression of miR169, miR395 and miR398 was repressed. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

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(Submitter supplied) gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL10892

40 Samples

Download data: GPR

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL10772 GPL10892 GPL6403

144 Samples

Download data: GPR

(Submitter supplied) gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL6403 GPL10892

120 Samples

Download data: GPR

(Submitter supplied) gen107_ptgs - chip in silencing suppressor plants or in mirna plants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - How are the histone modifications and the chromatin structure in miRNA mutants or in silencing suppressor plants?

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10772

24 Samples

Download data: GPR

(Submitter supplied) Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry

Organism:

Fragaria vesca

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16761

1 Sample

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. more...

Organism:

Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis arenosa x Arabidopsis thaliana; Arabidopsis suecica

Type:

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

5 related Platforms

58 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. more...

Organism:

Microlepia platyphylla; Salvinia molesta; Selaginella uncinata; Psilotum nudum; Cibotium barometz; Vandenboschia striata; Asplenium nidus; Salvinia cucullata; Azolla caroliniana; Palhinhaea cernua; Selaginella moellendorffii; Plenasium vachellii; Microsorum cuspidatum; Equisetum ramosissimum; Cyrtomium fortunei; Angiopteris fokiensis; Diplopterygium chinense; Pteris vittata; Lygodium japonicum; Odontosoria chinensis; Alsophila spinulosa; Diplazium esculentum; Ophioglossum vulgatum; Isoetes sinensis; Dicranopteris pedata

Type:

Non-coding RNA profiling by high throughput sequencing

25 related Platforms

26 Samples

Download data: FASTA

(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) Background miRNAs and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. Results We performed deep sRNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. more...

Organism:

Malus domestica

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15277 GPL15276

5 Samples

Download data: TXT