GEO DataSets

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of wild type and gemin2 Arabidopsis mutants plants exposed to 10ºC for 0, 1 and 24 hours.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19080

18 Samples

Download data: XLSX

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11221 GPL19080

24 Samples

Download data

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of gemin2 Arabidopsis mutant with wild type plants grown under continous light conditions

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11221

6 Samples

Download data: XLS

(Submitter supplied) Circadian clocks generate endogenous rhythms in most organisms from cyanobacteria to humans and facilitate entrainment to environmental diurnal cycles, thus conferring a fitness advantage. Both transcriptional and posttranslational mechanisms are prominent in the basic network architecture of circadian systems. Posttranscriptional regulation, including mRNA processing, is emerging as a critical step for the clock function. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: TXT

(Submitter supplied) Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila. Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day/night cycle1. more...

Organism:

Arabidopsis thaliana; Drosophila melanogaster

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL198 GPL1979 GPL6882

18 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to compare the transcriptional profile (RNA-seq) of lsm4 and lsm5 Arabidopsis mutants with their respective wild type plants grown under continous light conditions

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19080

24 Samples

Download data: XLSX

(Submitter supplied) We report the role of LSM2-8 complex in the Arabidopsis tolerance to abiotic stresses. LSM2-8 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieved over selected transcripts depending on stress nature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

8 Samples

Download data: TXT

(Submitter supplied) Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: TXT

(Submitter supplied) In plants, RNA polymerase II (Pol II) transcription of inverted DNA repeats produces hairpin RNAs that are processed by several DICER-LIKE enzymes into siRNAs that are 21-24-nt in length. When targeted to transcriptional regulatory regions, the 24-nt size class can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). In a forward genetic screen to identify mutants defective in RdDM of a target enhancer leading to TGS of a downstream GFP reporter gene in Arabidopsis thaliana, we recovered a structurally mutated silencer locus, named SΔ35S, in which the 35S promoter driving transcription of an inverted repeat of target enhancer sequences had been specifically deleted. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

1 Sample

Download data: TXT

(Submitter supplied) The early flowering Arabidopsis cäö mutant is defective in the BRR2a helicase involved in splicing. In order to get some explanation about the phenotype, we compared the expression profiles of wt and mutant with RNA-seq. In addtion, the same RNA-seq data was used to measure the extent of intron retention in the cäö mutant

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17311

6 Samples

Download data: TSV

(Submitter supplied) Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

32 Samples

Download data: TXT

(Submitter supplied) A better understanding of the mechanisms for plant in response to abiotic stresses is key for the improvement of plant to resistant to the stresses. Much has been known for the regulation of gene expression in response to salt stress at transcriptional level, however, little is known at posttranscriptional level for this response. Recently, we identified that SKIP is a component of spliceosome and is necessary for the regulation of alternative splicing and mRNA maturation of clock genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: TXT

(Submitter supplied) We report the role of SmE1 protein in the control of Arabidopsis development and tolerance to abiotic stresses. SmE1 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieve over selected transcripts depending on the stimulus nature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) A casual look at the behavior and function of animals and plants clearly shows that many physiological processes are periodic and tied to cyclical changes in a day. As suggested by the persistence of some rhythms in the absence of external cues, organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platforms:

GPL1979 GPL1980

24 Samples

Download data: CEL

(Submitter supplied) Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

18 Samples

Download data: TXT

(Submitter supplied) We apply 3'-End-RNA-seq based sequencing to globally quantify polyadenylation sites and transcript isoform abundance in human U-2 OS cells under wild-type and CPSF6 knock-down conditions at 3 different temperatures (32°C, 37°C and 39°C). We show that CPSF6 knock-down as well as temperature alterations lead to global changes in 3' UTR length and transcript abundance. By means of a differential response analysis with respect to temperature changes in wild type and temperature-decompensated CPSF6 knockdown cells, we reveal candidate genes underlying circadian temperature compensation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: TXT

(Submitter supplied) The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian oscillations transiently responding to a temperature change. Using a framework motivated by Floquet theory, we model the mRNA expression level of the fat body from Drosophila melanogaster following a step change from 25C to 18C. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

84 Samples

Download data: TSV

(Submitter supplied) The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian oscillations transiently responding to a temperature change. Using a framework motivated by Floquet theory, we model the mRNA expression level of the fat body from Drosophila melanogaster following a step change from 25C to 18C. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

73 Samples

Download data: TXT

(Submitter supplied) Homoeothermic organisms maintain their core body temperature in a narrow, tightly controlled range. Whether and how subtle circadian oscillations or disease-associated changes in core body temperature are sensed and integrated in gene expression programs remains elusive. Furthermore, a thermo-sensor capable of sensing the small temperature differentials leading to temperature-dependent sex determination (TSD) in poikilothermic reptiles has not been identified. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TXT