GEO DataSets

(Submitter supplied) Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15632

8 Samples

Download data: TXT

(Submitter supplied) Background: MicroRNAs regulate various biological processes in plants. Considerable data are available on miRNAs involved in the development of rice, maize and barley. In contrast, little is known about miRNAs and their functions in the development of wheat. In this study, five small RNA (sRNA) libraries from wheat seedlings, flag leaves, and developing seeds were developed and sequenced to identify miRNAs and understand their functions in wheat development. more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

5 Samples

Download data: FA

(Submitter supplied) Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). more...

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17701

72 Samples

Download data: XLS

(Submitter supplied) Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. more...

Organism:

Solanum tuberosum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15787

7 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) Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. more...

Organism:

Triticum turgidum subsp. durum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20257

96 Samples

Download data: TAB

(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) Purpose: To identify Fusarium wilt and salt-responsive miRNAs at genome wide level in Chickpea. Results: A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume specific miRNAs, miR5213, miR5232, miR2111 and miR2118 were found in all the libraries. The Poly (A) tailing assay based qRT-PCR was used to validate eleven conserved and five novel miRNAs. more...

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16348

3 Samples

Download data: TXT

(Submitter supplied) Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL28728 GPL20257

136 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNAs) are emerging as essential regulators of biological processes. Somatic embryogenesis is one of the most important techniques for gymnosperm breeding programs, but there is little understanding of its underlying mechanism. To investigate the roles of miRNAs during somatic embryogenesis in larch, we constructed a small RNA library from somatic embryos. High-throughput sequencing of the library identified 83 conserved miRNAs from 35 families, 16 novel miRNAs, and 14 plausible miRNA candidates, with a high proportion specific to larch or gymnosperms. more...

Organism:

Larix kaempferi

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13980

1 Sample

Download data: TXT

(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) Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. more...

Organism:

Triticum turgidum subsp. durum

Type:

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

Platforms:

GPL28728 GPL20257

134 Samples

Download data: XLSX

(Submitter supplied) In this study we performed a comprehensive analysis of miRNAs and their targets from peach fruit tissue using high-throughput sequencing combined with bioinformatics analysis and molecular experiments. A total of 557 known miRNAs and 275 putative novel miRNAs were predicted. 3959 and 1614 target genes for the 349 known and 193 novel miRNAs, respectively, were predicted where a single target gene could be targeted by different miRNAs, and a single miRNA can also have a large number of target genes. more...

Organism:

Prunus persica

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21993

2 Samples

Download data: XLSX

(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) 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) 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) 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) The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10467

2 Samples

Download data: TXT