GEO DataSets

(Submitter supplied) MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. more...

Organism:

Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20002

6 Samples

Download data: XLS

(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:

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 this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. more...

Organism:

Cercis gigantea (nom. inval.)

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL19878 GPL19879

2 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 play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. more...

Organism:

Prunus persica

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL17534

4 Samples

Download data: FA, TXT

(Submitter supplied) We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16345

4 Samples

Download data: TXT

(Submitter supplied) Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. more...

Organism:

Vitis labrusca x Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21492

2 Samples

Download data: TXT

(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) We report the high-throughput profiling of miRNAs in banana. By deep sequencing and computational and molecular analyses, we identify 113 known and 26 banana-specific miRNAs and we characterize their expression pattern under cold and heat stress. We find that 42 banana miRNAs are temperature-responsive. By degradome sequencing, we identify 60 targets for known miRNAs and half of these targets are regulated by 15 temperature-responsive miRNAs. more...

Organism:

Musa acuminata AAA Group

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21415 GPL21416

7 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) Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. more...

Organism:

Solanum lycopersicum

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL25655 GPL19694

36 Samples

Download data: XLSX

(Submitter supplied) Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant Camellia sinensis. MicroRNAs (miRNAs) have been known as key modulators of gene expression in defense responses; however, the role of miRNAs in tea plant during defensive responses to C. gloeosporioides remains unexplored. Six miRNA sequencing data sets and two degradome data sets were generated from C. more...

Organism:

Camellia sinensis

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL25554 GPL20107

8 Samples

Download data: TXT

(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) 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 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) Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. more...

Organism:

Malus hupehensis

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19425 GPL19426

3 Samples

Download data: TXT

(Submitter supplied) In this study, it is noticeable that 32 tea-specific miRNAs were confirmed on the base of genome survey, using deep sequencing and microarray hybridization, and many miRNAs might associate with secondary metabolites synthesis.

Organism:

Camellia sinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20107

1 Sample

Download data: TXT