GEO DataSets

(Submitter supplied) Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18580

4 Samples

Download data: TAB

(Submitter supplied) Vitis vinifera RNA degradome

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9396

1 Sample

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(Submitter supplied) Vitis vinifera endogenous small RNAs

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9396

4 Samples

Download data

(Submitter supplied) Pierce’s disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierce’s disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL1320

45 Samples

Download data: CEL

(Submitter supplied) MicroRNA (miRNA) is a class of functional non-coding small RNA with 19-25 nucleotides in length. Amur grape (Vitis amurensis Rupr.) is an important wild fruit crop with the strongest cold resistance in the Vitis genus and is used as an excellent breeding parent for grapevine, and with growing interest in terms of wine production. To date, there is a relatively large number of grapevine miRNAs (vv-miRNAs) from cultivated grapevine varieties such as Vitis vinifera L. more...

Organism:

Vitis amurensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14959

1 Sample

Download data: TXT

(Submitter supplied) Grapevine rupestris stem pitting-associated virus (GRSPaV) is a widespread virus affecting Vitis spp. Although it has established a compatible viral interaction in Vitis vinifera L. without the development of phenotypic alterations, it can occur as distinct variants that show different symptoms in diverse Vitis species. We investigated the changes induced by GRSPaV in V. vinifera cv Bosco, an Italian white grape variety, by combining agronomic, physiological, and molecular approaches, in order to provide comprehensive information about the global effects of GRSPaV. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL13936

18 Samples

Download data: PAIR

(Submitter supplied) Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15528 GPL18740

70 Samples

Download data: TXT

(Submitter supplied) Two independent small RNA (sRNA) libraries from male and female asparagus plants were sequenced, generating 4.13 and 5.88 million final cleaned reads, respectively. A total of 154 conserved miRNA belonging to 26 families, and 40 novel miRNA candidates that seemed to be specific to asparagus were identified, among them, 63 miRNAs exhibited significant differential expression between male and female plants, and 36 target mRNAs representing 44 conserved and fournovel miRNA in asparagus by high-throughput degradome sequencing analysis.

Organism:

Asparagus officinalis

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL20875

3 Samples

Download data: XLS

(Submitter supplied) MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. At present there is relatively little information regarding the role of miRNAs in the response to drought stress in maize. In this study, two small RNA libraries were sequenced, and a total of 11,973,711 and 14,326,010 raw sequences were generated from growing leaves of drought-tolerant and drought-sensitive maize seedlings, respectively. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: TXT

(Submitter supplied) Purpose: To identify high temperature, sailinity and drought-responsive miRNAs at genome wide level in B. juncea var varuna. Results: In this study four small RNA libraries viz. B. juncea control (BJC), B. juncea high temperature stressed (BJH), B. juncea salinity stressed (BJS) and B. juncea drought stressed (BJD) were prepared and sequenced. With the help of UEA sRNA workbench software package 51 conserved miRNAs belonging to 30 miRNA families were identified. more...

Organism:

Brassica juncea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16439

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) We present an efficient method to genome-wide discover new and drought stress responsive miRNAs in P. euphratica. High throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 189 new miRNAs which belonged to 120 families were identified, a large increasing to the number of P. euphratica miRNAs. Target prediction and degradome sequencing verification of 22 new and 21 conserved miRNA targets showed these targets were involved in multiple biological processes, including transcription regulation and response to stimulus. more...

Organism:

Populus euphratica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11262

2 Samples

Download data: FASTA, TXT

(Submitter supplied) Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

32 Samples

Download data: GTF, TXT

(Submitter supplied) Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (siRNAs). more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

50 Samples

Download data: TXT

(Submitter supplied) MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. Their action is generally mediated through complementary interactions with mRNA molecules - leading to their degradation or sequestration from the translational apparatus. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL7710

12 Samples

Download data: TXT

(Submitter supplied) Experimental research on the effects of abiotic stress over grapevine has mainly focused on water shortage. The adaptation of plants to stress is a complex response triggered by cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Approaches such as array-based transcript profiling allow assessing the expression of thousands of genes in control and stress tissues. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL11004

6 Samples

Download data: CEL

(Submitter supplied) In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities. An enrichment of 22-nt sRNA species was observed in leaf libraries. more...

Organism:

Saccharum hybrid cultivar (mixed); Saccharum hybrid cultivar SP90-3414; Saccharum hybrid cultivar CTC6

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18440 GPL16316 GPL18439

10 Samples

Download data: TXT

(Submitter supplied) microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18740

6 Samples

Download data: TXT