GEO DataSets

(Submitter supplied) We constructed four PARE libraries for the identification of miRNA target genes in Norway spruce.

Organism:

Picea abies

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19695

4 Samples

Download data: TXT

(Submitter supplied) The total RNA were extracted from pooled tissues of leaves and flowers from several plants of sacred lotus 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:

Nelumbo nucifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19280

2 Samples

Download data: TXT

(Submitter supplied) Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry

Organism:

Fragaria vesca

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16761

1 Sample

Download data: TXT

(Submitter supplied) Purpose:We aimed to characterize genome-widely the miRNA population and phasiRNA-generating genes/loci in litchi (Litchi chinensis). Multiple high throughput sequencing strategies, including sRNA sequencing, parallel analysis of RNA ends (PARE) sequencing, and strand-specific RNA-seq, were applied in combination with thorough bioinformatics analyses using a variety of computational methods.

Organism:

Litchi chinensis

Type:

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

Platforms:

GPL19467 GPL23452

12 Samples

Download data: TXT

(Submitter supplied) Small RNAs are a class of noncoding RNAs which are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasiRNAs. more...

Organism:

Arabidopsis thaliana; Medicago truncatula

Type:

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

Platforms:

GPL13222 GPL17491

50 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in rose. Here we carried out computational and experimental analysis of miRNAs, phased small interfering RNAs (phasiRNAs) and mRNAs in rose by analyzing 10 small RNA sequencing profiles from roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals of rose. more...

Organism:

Rosa rugosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24893

4 Samples

Download data: FASTA, XLS

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

Organism:

Rosa rugosa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24600 GPL24599

11 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs of rose. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in rose by analyzing 10 small RNA profiles from roots, petals, pollens, stamens, and leaves. more...

Organism:

Rosa rugosa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24599

10 Samples

Download data: TXT

(Submitter supplied) Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. more...

Organism:

Phaseolus vulgaris; Arachis hypogaea; Medicago truncatula; Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

22 Samples

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

Organism:

Persea americana; Petunia x hybrida; Solanum tuberosum; Setaria italica; Musa acuminata; Marsilea quadrifolia; Vitis vinifera; Cycas rumphii; Nuphar advena; Citrus sinensis; Ginkgo biloba; Carica papaya; Capsicum annuum; Lactuca sativa; Zea mays; Amborella trichopoda; Gossypium arboreum; Chlamydomonas reinhardtii; Volvox carteri; Picea abies; Cucurbita maxima; Solanum lycopersicum; Sorghum bicolor; Silene latifolia; Panicum virgatum; Chara corallina; Populus trichocarpa; Nicotiana tabacum; Erythranthe guttata; Hordeum vulgare; Triticum aestivum; Zostera marina; Aristolochia fimbriata; Miscanthus x giganteus

Type:

Non-coding RNA profiling by high throughput sequencing

34 related Platforms

99 Samples

Download data: TXT

(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Chara corallina thallus in different growing conditions. more...

Organism:

Chara corallina

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13437

3 Samples

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(Submitter supplied) Sequencing of sRNA and PARE libraries was performed for tissues collected from developmentally staged young panicles and anthers in rice variety Nongken 58

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

25 Samples

Download data: TXT

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

Organism:

Camellia sinensis

Type:

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

Platforms:

GPL25554 GPL19224

20 Samples

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(Submitter supplied) MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. more...

Organism:

Camellia sinensis

Type:

Other

Platform:

GPL25554

2 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. more...

Organism:

Camellia sinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19224

9 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. more...

Organism:

Camellia sinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19224

9 Samples

Download data: XLSX

(Submitter supplied) RNA-seq was used to characterize gene expression in soybean from a wide range of tissues. The primary focus of the project was small RNAs, and the identification of microRNAs and phased siRNA-generating loci, but RNA-seq data were generated from the same samples. This project was supported by the United Soybean Board.

Organism:

Glycine max

Type:

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

Platform:

GPL19246

16 Samples

Download data: TXT

(Submitter supplied) Small RNAs, including microRNAs and their targets, as well as phased secondary siRNAs, were characterized in the soybean genome by deep sequencing of small RNA libraries from a wide range of tissues. The mRNA targets of many of these small RNAs were also validated from many of the same tissues using PARE (Parallel Analysis of RNA Ends) libraries.

Organism:

Glycine max

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15008

78 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used.

Organism:

Solanum pennellii; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9245 GPL10776 GPL10777

18 Samples

Download data: FASTA

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

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27775

242 Samples

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