GEO DataSets

(Submitter supplied) MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis thaliana, 27 small RNA libraries were constructed and sequenced from various tissues, stresses and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

27 Samples

Download data: TXT

(Submitter supplied) To identify senescence-regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques. Parallel Analysis of RNA Ends (PARE) libraries were also constructed and sequenced to enable the large-scale examination of miRNA-guided cleavage products.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL13222

14 Samples

Download data: TXT

(Submitter supplied) Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9316 GPL9147

62 Samples

Download data

(Submitter supplied) The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using Parallel Analysis of RNA Ends (PARE) data is lacking in B. more...

Organism:

Brachypodium distachyon

Type:

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

Platform:

GPL17338

19 Samples

Download data: TXT

(Submitter supplied) miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. more...

Organism:

Arabidopsis thaliana; Oryza sativa; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

33 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11221 GPL9062

59 Samples

Download data: TXT

(Submitter supplied) Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11221

6 Samples

Download data: XLSX

(Submitter supplied) MicroRNAs are important regulatory molecules in most eukaryotes and the identification of their mRNA targets is essential for their functional analysis. From inflorescence tissue of Arabidopsis, >28,000,000 signatures were sequenced from 5’ ends of polyadenylated products of mRNA decay. Within the set of ~27,000 transcripts included in the 3,500,000 non-redundant signatures, several previously predicted but non-validated miRNA targets were found. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

7 Samples

Download data: TXT

(Submitter supplied) Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

5 Samples

Download data: TXT

(Submitter supplied) To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by Illumina’s technology. We identified some additional miRNAs, collateral miRNAs encoded in known miRNA precursors, phased smRNA clusters and nat-siRNAs. Organ specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

14 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL23157 GPL19580 GPL17639

24 Samples

Download data: BW, WIG

(Submitter supplied) MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23157

6 Samples

Download data: BW

(Submitter supplied) MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17639 GPL19580

18 Samples

Download data: BW, WIG

(Submitter supplied) To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in rice, we generated small RNA sequences from inflorescences from rice under control and under dought, salt, and cold stress treatments. Over 30 million reads were generated.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

4 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants，and increasing studies have been performed on some crops，however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. more...

Organism:

Gossypium hirsutum

Type:

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

Platform:

GPL16101

4 Samples

Download data: TXT

(Submitter supplied) In our study, small RNA library and degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis, and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. more...

Organism:

Glycine max

Type:

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

Platform:

GPL11192

2 Samples

Download data: TXT

(Submitter supplied) One of the major players controlling RNA decay is the cytoplasmic 5'-to-3' exoribonuclease, which is conserved among eukaryotic organisms. In Arabidopsis, the 5'-to-3' exoribonuclease XRN4 is involved in disease resistance, the response to ethylene, RNAi, and miRNA-mediated RNA decay. Curiously, XRN4 appears to display selectivity among its substrates because certain 3' cleavage products formed by miRNA-mediated decay, such as from ARF10 mRNA, accumulate in the xrn4 mutant, whereas others, such as from AGO1, do not. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL, TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. At present there is relatively little information regarding the role of miRNAs in the response to drought stress in maize. In this study, two small RNA libraries were sequenced, and a total of 11,973,711 and 14,326,010 raw sequences were generated from growing leaves of drought-tolerant and drought-sensitive maize seedlings, respectively. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: TXT

(Submitter supplied) Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL71

37 Samples

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(Submitter supplied) Conventional RNA interference (RNAi) pathways suppress eukaryotic gene expression at the post-transcriptional or transcriptional level. At the core of RNAi are small RNAs (sRNAs) and effector Argonaute proteins. Arabidopsis AGO1 is known to bind microRNAs (miRNAs) and post-transcriptionally repress target genes via mRNA cleavage and/or translational inhibition in the cytoplasm. Here, we report that AGO1 binds to the chromatin of transcriptionally active genes and promotes their transcription. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

94 Samples

Download data: BEDGRAPH, BIGWIG, MATRIX, TXT