GEO DataSets

(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

(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) 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:

GPL18740 GPL15528

70 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

3 Samples

Download data: TXT

(Submitter supplied) De-multiplexing the unique identifiers discovered data consisted of 28,808,716 clean reads from fruit samples at 40 DAF, 27,941,132 reads from 65 DAF, and 25,457,565 reads from fruit sample at 90 DAF.

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18580

3 Samples

Download data: XLSX

(Submitter supplied) Vitis vinifera RNA degradome

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9396

1 Sample

Download data

(Submitter supplied) Vitis vinifera endogenous small RNAs

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9396

4 Samples

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(Submitter supplied) We were interested in changes in small RNA abundance changes in response to developmental transitions in Arabidopsis thaliana shoots, with special focus on vegetative phase change. We specifically wanted to separate the temporal changes in gene expression that result from vegetative phase change and those from flowering. Because of the close timing between the juvenile-to-adult and adult-to-reproductive developmental transitions in Arabidopsis grown under long day conditions, we used the late-flowering genotype FRI;FLC developed by the lab of Richard Amasino by introgressing the FRI allele from Sf-2 into the Col-0 genetic background, which is fri;FLC. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

28 Samples

Download data: TXT

(Submitter supplied) High-throughput sequencing was employed to identify conserved and variable microRNAs among 4 Rosa

Organism:

Rosa rugosa; Rosa hybrid cultivar

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15889 GPL15890

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) Background: The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety ‘Norton’, with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. more...

Organism:

Vitis vinifera; Vitis sp. cv. 'Norton'

Type:

Expression profiling by array

Platform:

GPL11004

18 Samples

Download data: CEL

(Submitter supplied) Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL13936

171 Samples

Download data: PAIR

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

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL15632 GPL17701

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) 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

(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) Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The roles of microRNAs (minRNAs) in mRNA destabilization and translational repression of this disease are well appreciated, their involvement in endonucleolytic cleavage of target mRNAs is poorly understood. Methods: High throughput small RNA sequencing was employed for the identification and profiling of miRNAs by six pairs of colorectal cancer tissues (CT) and their adjacent tissues (CN). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: XLSX