GEO DataSets

(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) 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) 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 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:

GPL17639 GPL13222

6 Samples

Download data: TXT

(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) RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5’ end to the 3’ end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. more...

Organism:

Arabidopsis thaliana

Type:

Other

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) 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

140 Samples

Download data

(Submitter supplied) Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: CSV

(Submitter supplied) Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

128 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; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

13 Samples

Download data: TXT

(Submitter supplied) The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

5 Samples

Download data: TXT

(Submitter supplied) The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

8 Samples

Download data: TXT

(Submitter supplied) To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL24270

24 Samples

Download data: BEDGRAPH, DIFF

(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) 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) Analysis of atsf1-2 mutant seedlings for pre-mRNA splicing defect. The atsf1-2 mutant is a homozygous T-DNA insertion line isolated from a SALK line, SALK_062177. Results identify transcripts with altered alternative splicing pattern in the atsf1-2 mutant. We used microarrays to examine the transcriptome profile in the atsf1-2 mutant and identified genes of which transcript levels were changed significantly.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL, CHP

(Submitter supplied) The processing of Arabidopsis thaliana microRNAs (miRNAs) from longer primary transcripts (pri-miRNAs) requires the activity of several proteins, including DICER-LIKE1 (DCL1), the double stranded RNA binding protein HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). It has been noted before that the morphological appearance of weak se mutants is reminiscent of plants with mutations in ABH1/CBP80 and CBP20, which encode the two subunits of the nuclear cap-binding complex. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL1980

12 Samples

Download data: CEL