GEO DataSets

(Submitter supplied) Purpose: The goals of this study are to detect the small RNAs generated from the PMS1T gene and the cleavage sites mediated by small RNAs (microRNAs or phasiRNAs). Methods: The rice panicles were collected in liquid nitrogen and their total RNA were extracted for library construction and subsequent sequencing on an Illumina HiSeq 2000. Results: Using an optimized data analysis workflow, we mapped a series of small RNAs generated from the PMS1T region of the rice genome; most of these small RNAs were 21-nt phasiRNAs. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL13834

36 Samples

Download data: TXT

(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) 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) Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for traits of agronomic importance like male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, play an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein which acts as a cofactor of MSP1 in the same regulatory pathway. more...

Organism:

Oryza sativa

Type:

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

Platform:

GPL13160

54 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) 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) 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 osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

6 Samples

Download data: TXT

(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) 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) Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

12 Samples

Download data: CEL, TXT

(Submitter supplied) In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

4 Samples

Download data

(Submitter supplied) The maize ocl4 mutants showed differing levels of male sterility, which seems correlating with the quantity of 21-nt phasiRNA remaining during pre-meiotic stage. In this case, sRNA and transcriptome was profiled and compared in this study, showed that OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers.

Organism:

Zea mays

Type:

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

Platform:

GPL15463

16 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) 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

(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 subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

5 Samples

Download data: 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 subsp. mays; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15463 GPL17914

89 Samples

Download data: 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 subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

6 Samples

Download data: TXT

(Submitter supplied) To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from root apices (RoApx), shoot apices (ShApx), developing inflorescence (Infl) and mature leaf (Leaf). These tissues were chosen because they are expected to be rich in small RNAs and display different patterns of small RNA expression. The RoApx, ShApx, and Infl samples are expected to be enriched for meristematic tissues each of which have different fates. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9388

12 Samples

Download data: FNA, QUAL, TXT