GEO DataSets

Analysis of leaves from transgenics overexpressing microRNA miR319a. Most plant miRNAs have perfect or near-perfect complementarity with their targets. However, targets with up to five mismatches exist. Results provide insight into the mechanistic basis of target recognition by plant miRNA.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL198

Series:

GSE2081

4 Samples

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(Submitter supplied) jaw-D plants grown in SD compared to columbia wt. Keywords: parallel sample

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2066

Platform:

GPL198

4 Samples

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(Submitter supplied) RNA was isolated from vegetative apices of 7d-old short-day grown plants. Overexpression of miR164b and miR172a versus control. Keywords: parallel sample

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2065

Platform:

GPL198

6 Samples

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(Submitter supplied) RNA was harvested from floral apices of long-day grown plants. Overexpression of miR156b and 164b versus control. Keywords: parallel sample

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2064

Platform:

GPL198

6 Samples

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(Submitter supplied) Flowers stage 15: Comparison of miR159a overexpressers to empty-vector control. Keywords: parallel sample

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2063

Platform:

GPL198

6 Samples

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Analysis of vegetative apices of transgenics overexpressing miRNA miR164b or miR172a. Most plant miRNAs have perfect or near-perfect complementarity with their targets. However, targets with up to 5 mismatches exist. Results provide insight into the mechanism of target recognition by plant miRNA.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 3 genotype/variation sets

Platform:

GPL198

Series:

GSE2080

6 Samples

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Analysis of floral apices of transgenics overexpressing miRNA miR156b or miR164b. Most plant miRNAs have perfect or near-perfect complementarity with their targets. However, targets with up to 5 mismatches exist. Results provide insight into the mechanism of target recognition by plant miRNA.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 3 genotype/variation sets

Platform:

GPL198

Series:

GSE2079

6 Samples

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Analysis of stage 15 flowers from transgenics overexpressing miRNA miR159a. Most plant miRNAs have perfect or near-perfect complementarity with their targets. However, targets with up to five mismatches exist. Results provide insight into the mechanistic basis of target recognition by plant miRNA.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL198

Series:

GSE2078

6 Samples

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(Submitter supplied) Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by MPSS

Platform:

GPL2675

4 Samples

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(Submitter supplied) MicroRNAs (miRNAs) are noncoding RNAs of approximately 22 nucleotides in length that usually suppress the translation of target messenger RNAs (mRNAs) through partial complementarity to the 3¡¦ untranslated region (3¡¦ UTR) of protein-coding mRNAs in animals. However, there is increasing evidence that miRNAs can also reduce the steady-state levels of their target mRNAs in animals. In this investigation, both miRNA and mRNA profiles from the undifferentiated human embryonic stem cell line hES-T3 (T3ES), hES-T3 derived embryoid bodies (T3EB) and hES-T3 differentiated fibroblast-like cells (T3DF) were quantitatively determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9147

1 Sample

Download data: TXT

(Submitter supplied) We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis ago1-25 and hyl1-2 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10978 GPL10977

18 Samples

Download data: CEL, TXT

(Submitter supplied) Oryza sativa cv. Nipponbare was engineered to over-express a barley alanine aminotransferase (alaAT) gene using the promoter (OsANT1) from a rice aldehyde dehydrogenase gene that expresses in roots. We are using biotechnology to improve the nitrogen use efficiency of rice by over-expressing alaAT in a tissue specific (root) manner. The AlaAT enzyme is a reversible aminotransferase that is linked to both C and N metabolism since it uses pyruvate plus glutamate to produce alanine and 2-oxoglutarate, and visa versa.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

32 Samples

Download data: CEL

(Submitter supplied) In plants, the known microRNAs (miRNAs) are produced as ~21 nucleotide (nt) duplexes from their precursors by Dicer like 1 (DCL1). They are incorporated into Argonaute 1 (AGO1) protein to regulate target gene expression primarily through mRNA cleavage. We report here the discovery of a new class of miRNAs in the model monocot rice (Oryza sativa). These are 24 nt in length and require another member of the Dicer family, DCL3, for their biogenesis. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

7 Samples

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(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) Small RNA expression from Nicotiana benthamiana leaves was profiled with the primary goal of ascertaining microRNA isoform diversity for known, conserved families. A secondary goal was to provide a baseline small RNA expression atlas for this species and tissue.

Organism:

Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17448

4 Samples

Download data: TXT

(Submitter supplied) Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition is primarily determined by pairing of the miRNA seed sequence (nucleotides 2–8) to complementary match sites in each mRNA target. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

15 Samples

Download data: TXT

(Submitter supplied) miRNAs play important roles in every aspect of plant development. Small RNA regulation confers sensitivity and robustness onto gene regulatory networks, and the morphogen-like readout of small RNA mobility gradients yields sharply delineated domains of target gene expression. However, how the spatiotemporal patterns of miRNA activity are attained is less well understood. We used the high-resolution maize shoot apex transcriptome atlas (Knauer et al., 2019) together with data from small RNA-Seq, PARE analysis, small RNA in-situ hybridization, and RNAseq of weak dcl1 mutant tissues to demonstrate that miRNA accumulation and function during development is regulated in a tiissue dependent manner at the transcriptional and post-transcriptional level.

Organism:

Zea mays

Type:

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

Platforms:

GPL15463 GPL17628

9 Samples

Download data: TXT