GEO DataSets

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under normal growth conditions to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

6 Samples

Download data: CEL, TXT

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

6 Samples

Download data: CEL, TXT

(Submitter supplied) Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rcf1-1 mutation on global gene expression with or without cold stress at 4°C. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) Plants adapt to abiotic and biotic stresses by activating abscisic acid-mediated (ABA) abiotic stress-responsive and salicylic acid-(SA) or jasmonic acid-mediated (JA) biotic stress-responsive pathways, respectively. Although the abiotic stress-responsive pathway interacts antagonistically with the biotic stress-responsive pathways, the mechanisms that regulate these pathways remain largely unknown. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7299

8 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL9020 GPL198

24 Samples

Download data: CEL, TXT

(Submitter supplied) The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL9020

12 Samples

Download data: TXT

(Submitter supplied) To understand the role of STCH4 in cold-responsive gene regulation

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

18 Samples

Download data: TXT

(Submitter supplied) In Arabidopsis, CBFs transcription factors (CBF1, CBF2 and CBF3) play fundamental roles in plant cold tolerance, especially in cold-acclimation. By employing CRISPR/Cas9, we knocked out CBF1 and CBF2 simultaneously in cbf3 background and generated cbfs triple mutant. This mutant facilitated the discovery of CBF-regulated genes. In this study, Arabidopsis 14-d-old Col-0 and cbfs mutant were treated with cold stress (4 degree centigrade) for 0, 3 and 24 hours. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: TXT

(Submitter supplied) Sequencing of mRNA extracted from 14 day old Columbia and hos1-3 seedlings grown at 22°C 12:12 light dark Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: DIFF, FPKM_TRACKING

(Submitter supplied) The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

18 Samples

Download data: CSV

(Submitter supplied) The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes with the CBF pathway being knocked out, we showed the CBF pathway plays a significant role in natural variation of freezing tolerance.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

44 Samples

Download data: CSV

(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) Salicylic acid (SA) levels increase in Arabidopsis upon exposure to low temperature for more than a week. This cold-induced SA biosynthesis was found to proceed through the isochorismate synthase (ICS) pathway. The sid2-1 mutant is deficient in ICS1 and does not make SA at low temperature. We used microarray analysis to examine the genes differentially regulated by low temperature that were dependent on SA

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

12 Samples

Download data: CEL

(Submitter supplied) CAMTA3 is known to be involved in regulation of induction of early cold-responsive genes, CBF1 and CBF2 at cold conditions and of suppression of SA production at warm temperature. Considering a functional redundancy of CAMTA family members in both warm and cold conditions, high-order of camta mutants, camta double and triple mutants, were generated and used to determined the effects of their regulation using microarray analysis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

21 Samples

Download data: CEL

(Submitter supplied) Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7725

24 Samples

Download data: GPR

(Submitter supplied) To identify chloroplastic H2O2-responseive genes, an estrogen-inducible RNAi method was used for silencing of tAPX, a H2O2-scavenging enzyme in chloroplasts. At 48 h after treatment with estrogen, the expression of tAPX was silenced in the IS-tAPX-19-23 plants, but not in the IS-GUS-2-17 plants (negative control), resulting a large change in gene expression. These genes are candidates for chloroplastic H2O2-responseive genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7299

4 Samples

Download data: 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 functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL