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Links from GEO DataSets

Items: 20

1.

STCH4/REIL2 confers cold stress tolerance in Arabidopsis by promoting rRNA processing and CBF protein translation

(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
Series
Accession:
GSE141304
ID:
200141304
2.

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platforms:
GPL198 GPL9020
24 Samples
Download data: CEL, TXT
Series
Accession:
GSE63186
ID:
200063186
3.

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Affymetrix]

(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
Series
Accession:
GSE63185
ID:
200063185
4.

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Agilent]

(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
Series
Accession:
GSE63184
ID:
200063184
5.

Functions of Arabidopsis REI1-LIKE cytosolic ribosome biogenesis factor homologs

(Submitter supplied) Functions of Arabidopsis REI1-LIKE (REIL) proteins, two homologs of a yeast ribosome biogenesis protein (RBP) that takes part in the late cytoplasmic steps of 60S ribosomal subunit maturation, were characterized by systems analyses of the 10°C cold acclimating reil1-1 reil2-1 double mutant compared to Col-0 wildtype. The mutant lacked both REIL proteins, was strongly growth inhibited in the cold and complemented by constitutive expression of N-terminal FLUORESCENT PROTEIN (FP)-REIL1 and FP-REIL2 fusion proteins under control of the UBIQUITIN 10 promoter. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL9020
29 Samples
Download data: TXT
Series
Accession:
GSE101111
ID:
200101111
6.

RNA-seq data for Arabidopsis cbfs-1

(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
Series
Accession:
GSE130729
ID:
200130729
7.

Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.

(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
Series
Accession:
GSE41378
ID:
200041378
8.

Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.

(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
Series
Accession:
GSE41377
ID:
200041377
9.

The rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress.

(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
Series
Accession:
GSE39090
ID:
200039090
10.

Expression data from WT, sid2-1

(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
Series
Accession:
GSE43819
ID:
200043819
11.

Expression data from WT, camta1/2, camta1/3, camta2/3, camta1/2/3 mutants

(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
Series
Accession:
GSE43818
ID:
200043818
12.

Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

(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
Series
Accession:
GSE106284
ID:
200106284
13.

Potential role of natural variation in the Arabidopsis CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

(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
Series
Accession:
GSE67332
ID:
200067332
14.

Transcriptomic analysis of the voz1 voz2 double mutant

(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
Series
Accession:
GSE24741
ID:
200024741
15.

Arabidopsis cold regulated transcriptome, translatome and CSP1 RNA regulon

(Submitter supplied) Transcriptome, translatome, and CSP1 RNA regulon analysis of 25-d-o Arabidopsis rosettes exposed to 12h low temperature (4C) treatment.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
38 Samples
Download data: CEL
Series
Accession:
GSE38030
ID:
200038030
16.

Gene Expression Comparing Col to WS to Identify conserved cold-responsive Affymetrix signatures

(Submitter supplied) Gene expression Arabidopsis 24h cold-treated, 4c, seedlings to identify a *gold-standard* set of cold-responsive transcripts. Most of the CBF overexpression lines are in WS, therefore, it is necessary to identify a consistent set of transcripts that are detectible as cold-induced on the ATH1 platform for both WS and Columbia, so that appropriate comparisons can be made to determine the effects of low temperature in CBF overexpressing or loss of function plants in a WS background and an attempt can be made to compare the results of altered CBF function to published microarray studies. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
9 Samples
Download data: CEL
Series
Accession:
GSE64575
ID:
200064575
17.

Expression data from WT and transgenic plants overexpressing cold-induced transcription factors

(Submitter supplied) Our goal in this study is to understand the regulation mechanism of genes including CBF regulon in low temperature. We addressed these issues by overexpressing the transcription factors encoded by genes that are rapidly induced in parallel with the CBF genes. The results show that the low temperature regulatory network is highly interconneted.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
28 Samples
Download data: CEL
Series
Accession:
GSE55907
ID:
200055907
18.

Expression data from WT (Ws-2), CBF1,2,3, and CBF2Δc (a truncated CBF2) overexpression

(Submitter supplied) CBF1, CBF2 and CBF3 regulons comprise nearly identical gene sets The vast majority of CBF2 regulon genes were down-regulated less that 50% by overexpression of CBF2Δc, a truncated version of CBF2
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
28 Samples
Download data: CEL
Series
Accession:
GSE55906
ID:
200055906
19.

Low R:FR treatment at 16 and 22 degrees

(Submitter supplied) The purpose of this experiment was to identify genes responding differently to a 24 h low red to far red ratio (R:FR) treatment in plants grown at 16 and 22 degrees Keywords: Light treatment
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
4 Samples
Download data: CEL
Series
Accession:
GSE8745
ID:
200008745
20.

RNAseq data of two week-old soybean leaves response to cold stress

(Submitter supplied) Transcriptome analysis of cold-treated leaves (unifoliates) of soybean seedlings were performed. RNAseq analysis was performed using two lanes on a Illumina HiSeq2000 and sequenced on a 100bp, paired-end run.
Organism:
Glycine max
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15008
9 Samples
Download data: TXT
Series
Accession:
GSE117686
ID:
200117686
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