GEO DataSets

(Submitter supplied) To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

4 Samples

Download data: TXT

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

Organism:

Embryophyta; Camellia sinensis

Type:

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

Platforms:

GPL18106 GPL19224

11 Samples

Download data: TXT, XLSX

(Submitter supplied) We discovered 31 up-regulated miRNAs and 43 down-regulated miRNAs in ‘Yingshuang’, and 46 up-regulated miRNA and 45 down-regulated miRNAs in ‘Baiye 1’ in response to cold stress, respectively. A total of 763 related target genes were detected by degradome sequencing. The RLM-5’RACE procedure was successfully used to map the cleavage sites in six target genes of C. sinensis. These findings reveal important information about the regulatory mechanism of miRNAs in C. more...

Organism:

Camellia sinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19224

3 Samples

Download data: XLSX

(Submitter supplied) Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. more...

Organism:

Camellia sinensis; Embryophyta

Type:

Non-coding RNA profiling by array

Platform:

GPL18106

8 Samples

Download data: 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) Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. more...

Organism:

Saccharum hybrid cultivar SP70-1143

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16317

4 Samples

Download data: TXT

(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) Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 253 potential candidate miRNAs were identified, and among them 48 novel miRNAs/ novel members of known miRNA families whose complementary miRNAs were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. more...

Organism:

Medicago truncatula

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9315

2 Samples

Download data: TXT

(Submitter supplied) To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4°C/4°C for 1h，4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25°C/20°C for 1h，4h, 8h, 12h, 24h and 48h)leaves of LA1777’ (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. more...

Organism:

Solanum habrochaites

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL18655

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) Expression profiles were analyzed between drought stress and normal watered control at the tillering and inflorescence stages.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by array

Platform:

GPL8015

10 Samples

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(Submitter supplied) MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants，and increasing studies have been performed on some crops，however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. more...

Organism:

Gossypium hirsutum

Type:

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

Platform:

GPL16101

4 Samples

Download data: TXT

(Submitter supplied) Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. more...

Organism:

Salicornia europaea

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19315

6 Samples

Download data: FA

(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) 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) In our study, small RNA library and degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis, and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. more...

Organism:

Glycine max

Type:

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

Platform:

GPL11192

2 Samples

Download data: TXT

(Submitter supplied) The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. more...

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19279

2 Samples

Download data: TXT