GEO DataSets

(Submitter supplied) As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. more...

Organism:

Zea mays

Type:

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

Platforms:

GPL15463 GPL20156

18 Samples

Download data: XLSX

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

Organism:

Zea mays subsp. parviglumis; Zea mays subsp. mays; Zea mays subsp. mexicana; Zea luxurians

Type:

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

4 related Platforms

216 Samples

Download data: TSV

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...

Organism:

Zea mays subsp. mays

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL34147

11 Samples

Download data: TXT

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...

Organism:

Zea mays subsp. parviglumis; Zea mays subsp. mexicana; Zea luxurians; Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

4 related Platforms

136 Samples

Download data: TSV

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...

Organism:

Zea mays subsp. parviglumis; Zea mays subsp. mays; Zea mays subsp. mexicana; Zea luxurians

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

69 Samples

Download data: TXT

(Submitter supplied) We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. more...

Organism:

Zea mays

Type:

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

Platform:

GPL15463

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

Organism:

Citrullus lanatus

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23842 GPL20225

15 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...

Organism:

Citrullus lanatus

Type:

Other

Platform:

GPL23842

1 Sample

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. more...

Organism:

Citrullus lanatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20225

14 Samples

Download data: TXT

(Submitter supplied) In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection (LCM), we analyzed tapetal cells, meiocytes, and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL27775

18 Samples

Download data: TXT

(Submitter supplied) Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. more...

Organism:

Panax notoginseng

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23359

7 Samples

Download data: TXT

(Submitter supplied) The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) 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:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19279

2 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) In grasses, phased small interfering RNAs (phasiRNAs), 21- or 24-nucleotide (nt) in length, are predominantly expressed in anthers and regulate male fertility. However, their targets and mode of action on the targets remain unknown. Here we profile phasiRNA expression in premeiotic and meiotic spikelets as well as in purified male meiocytes at early prophase I, tetrads and microspores in rice. We show that 21-nt phasiRNAs are most abundant in meiocytes at early prophase I while 24-nt phasiRNAs are more abundant in tetrads and microspores. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL24468

65 Samples

Download data: TXT, XLSX

(Submitter supplied) Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants. Monocots generate 21- and 24-nt phasiRNAs by miR2118 and miR2275 respectively from noncoding RNAs with spatial-temporal specificity during anther development. However, which ARGONAUTES (AGOs) associate with these two miRNAs remains elusive. Here we show that rice AGO1d, specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL27660

90 Samples

Download data: CSV, TXT

(Submitter supplied) Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

31 Samples

Download data: TXT

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

Organism:

Zea mays subsp. mays; Zea mays

Type:

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

Platforms:

GPL15463 GPL17914

100 Samples

Download data: TXT