GEO DataSets

(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) 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) 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) 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

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

Download data

(Submitter supplied) microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. Here, we perform a comprehensive analysis of miRNAs in the zoonotic parasite E. canadensis G7, one of the causative agents of the neglected disease cystic echinococcosis. Small RNA libraries from protoscoleces and cyst walls of E. more...

Organism:

Echinococcus canadensis; Echinococcus granulosus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18185 GPL19605

6 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) We performed extensive transcriptome analysis of the tiger pufferfish (Takifugu rubripes) using the next-generation sequencer SOLiD III, and profiled millions of small RNA sequences in somatic tissues and gonads, as well as identifying thousands of miRNAs. The number of miRNAs identified was the highest in fish species reported to date. We also report highly variable isomiR features.

Organism:

Takifugu rubripes

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19713

9 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. more...

Organism:

Cunninghamia lanceolata

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18151

3 Samples

Download data: FA

(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) Purpose: The goal of this study is to detect the environmental influence on small RNAs population (miRNAs and other smallRNAs) in berries from two different grapevine varieties, evaluating Genotype x Environment interactions. Methods: The grapevine berries were collected in liquid nitrogen and their small RNA fractions were isolated from total RNA for library construction and subsequent sequencing on an Illumina HiSeq 2000. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18740

48 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) MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotic animals. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown. Using Illumina deep-sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. more...

Organism:

Echinococcus granulosus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18185

3 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10850 GPL13497 GPL11154

48 Samples

Download data: TXT

(Submitter supplied) For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL10850

8 Samples

Download data: TXT

(Submitter supplied) For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL10850

7 Samples

Download data: TXT

(Submitter supplied) For the further examination of cell cycle dependent gene expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent gene expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

8 Samples

Download data: TXT

(Submitter supplied) For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: XLSX

(Submitter supplied) For the further examination of cell cycle dependent gene expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent gene expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

8 Samples

Download data: TXT