GEO DataSets

(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) 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) 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) In this study, we analyzed the pre-mRNA splicing status in wild-type Col, atprmt5 mutants, and two atprmt5 suppressors (m90 and s215). RNA-seq analyses revealed that m90 and s215 can partially rescue the pre-mRNA splicing defects in atprmt5 mutants. Further study showed that m90 and s215 were identified in the highly conserved pre-mRNA splicing factor 8 (AtPrp8) and demonstrated that Prp19C/NTC complex failed to be assembled into U5 snRNP to form activated spliceosome in atprmt5 mutants, while restored in the suppressor. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BW, TXT

(Submitter supplied) Introns are removed by the spliceosome, a large complex composed of five ribonucleoprotein subcomplexes (U snRNP). In metazoans, the U1 snRNP, which binds to 5’ splice sites, also fulfills regulatory roles in splice site selection and possesses non-splicing related functions. Here, we show that an Arabidopsis U1 snRNP subunit, LUC7, affects constitutive and alternative splicing. Interestingly, LUC7 specifically promotes splicing of a subset of terminal introns. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TAR

(Submitter supplied) Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

2 Samples

Download data: XLSX

(Submitter supplied) Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: XLSX

(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) Characterization of the lsm1a lsm1b transcriptional profile. LSM1 protein is involved in RNA decay through decapping facilitation. The performed array help us to understand the transcription level alterations produced by the absence of LSM1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

3 Samples

Download data: GPR

(Submitter supplied) Characterization of gene expression and intron retention in lsm8-1 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

1 Sample

Download data: BAR, CEL

(Submitter supplied) This GEO submission includes RNAseq raw data (fastq) and processed data (using ASpli 1.6.0) from samples obtained in the wild type and the single prefoldin4 and lsm8 mutants in three different environmental conditions as well as in the triple prefoldin2 prefoldin4 prefoldin6 mutant growth in standard conditions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19580

28 Samples

Download data: TAB

(Submitter supplied) We report the role of LSM1-7 complex in the Arabidopsis tolerance to abiotic stresses. LSM1-7 controls gene expression reprogramming at the post-transcriptional level by promoting the decapping of mRNA. This function is selectively achieve over selected stress-induced transcripts depending on stress nature.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

6 Samples

Download data: TXT

(Submitter supplied) We report the application of illumina high throughput RNA sequencing for rrc1-3 mutants in both light and dark conditions(three replicates under each condition) in Arabidopsis. By obtaining over 100 million reads (150bp paired_end) for each rRNA depleted lib, we compared the transcriptome profile between rrc1-3 mutant and Col-0 wild type light and dark conditions. We find that genome wide spliciing activities are general defective in rrc1-3 mutant comparing to Col-0 wild type, which indicates the importance of post-transcriptional processing on gene expression regulation. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21785 GPL21179

12 Samples

Download data: XLSX

(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) In plants, many gene transcripts are very unstable, which is important for the tight control of their temporal and spatial expression patterns. To identify cellular factors controlling the stability of unstable mRNAs in plants, we used luciferase imaging in Arabidopsis to isolate a recessive mutant, stabilized 1 (sta1), with enhanced stability of the normally unstable luciferase transcript. The sta1 mutation also causes the stabilization of some endogenous gene transcripts and has a range of developmental and stress response phenotypes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2102

Platform:

GPL198

7 Samples

Download data: CEL, EXP

Analysis of sta1-1 seedlings mutant for the pre-mRNA splicing factor STABILIZED1. sta1-1 mutant identified in a screen for mutants with enhanced stability of the normally unstable luciferase transcript. Results identify endogenous genes with enhanced transcript stability in the sta1-1 mutant.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL198

Series:

GSE4662

7 Samples

Download data: CEL, EXP

(Submitter supplied) In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10272

2 Samples

Download data: BEDGRAPH

(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 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