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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of Arabidopsis plants that overexpress green fluorescent protein (GFP) and GFP-LOV kelch protein 2 (GFP-LKP2)

ABSTRACT: LKP2 belongs to a group of blue light receptors in Arabidopsis thaliana. We performed DNA microarray analysis to identify genes whose expression levels are altered in LKP2-overexpressing plants. Agilent's Whole Arabidopsis Genome Oligo Microarray (G2519F, V4, 4x44K) was used. Comparison between 35S:GFP overexpressing- and 35S:GFP-LKP2 overexpressing- plants (Yasuhara et al. 2004) was performed.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yuji Miyazaki

PROVIDER: E-GEOD-37197 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome analysis of Arabidopsis plants that overexpress green fluorescent protein (GFP) and GFP-LOV kelch protein 2 (GFP-LKP2)

Project description:LKP2 belongs to a group of blue light receptors in Arabidopsis thaliana. We performed DNA microarray analysis to identify genes whose expression levels are altered in LKP2-overexpressing plants. Agilent's Whole Arabidopsis Genome Oligo Microarray (G2519F, V4, 4x44K) was used.

2012-04-25 | GSE37197 | GEO

Arabidopsis SKD1 Proteom LC-MSMS

Project description:We investigated the heat-dependent in-vivo interactome of Arabidopsis thaliana SKD1 using a transgenic 35S::GFP-SKD1 line. Potential interactors of GFP-SKD1 were co-immunoprecipitated from cell extracts of untreated or heat-treated rosette leaves and analyzed by mass spectrometry. A line overexpressing free YFP (35S::YFP) was used as a negative control. For each genotype and condition, proteins of three biological replicates were analyzed. An in-solution digest was performed on the beads, and peptides were subjected to liquid chromatography and tandem mass spectrometry (LC-MS/MS, Dr. S. Müller, CECAD/CMMC Proteomics Facility Cologne).

2021-06-23 | PXD025028 | Pride

Transcript profiling of Arabidopsis thaliana transgenic seedlings constitutively overexpressing UGT74E2 (35S::UGT74E2).

Project description:Transcript profiling of transgenic Arabidopsis thaliana seedlings constitutively overexpressing UGT74E2 (35S::UGT74E2).

2009-09-19 | E-MEXP-2358 | biostudies-arrayexpress

Transcription profiling of wild type and DREB2C over-expression Arabidopsis plants

Project description:We analysed DREB2C overexpressing Arabidopsis plants (35S:DREB2C-a line: S15, 35S:DREB2C-c line: S22)with cDNA microarray (A-MEXP-187).

2007-03-10 | E-MEXP-986 | biostudies-arrayexpress

Expression data of seeds imbibed at 22˚C or 4˚C for 24hr of Arabidopsis thaliana

Project description:Keeping imbibed seeds at low temperatures for a certain period, so called seed vernalization (SV) treatment, promotes seed germination and subsequent flowering in various plants. Vernalization-promoting flowering requires GSH. However, the expression patterns analyzed by GeneChip arrays showed that increased GSH biosynthesis partially mimics SV treatment in Arabidopsis thaliana. SV treatment (keeping imbibed seeds at 4°C for 24 h) induced a specific pattern of gene expression and promoted subsequent flowering in wild-type plants. A similar pattern was observed at 22°C in transgenic plants (35S-GSH1 plants) overexpressing the γ-glutamylcysteine synthetase gene GSH1, coding an enzyme limiting GSH biosynthesis, under the control of the cauliflower mosaic virus 35S promoter. This pattern was strengthened at 4°C but flowering was less responsive to SV treatment. There was a difference in the transcript behaviour of the flowering repressor FLC between wild-type and 35S-GSH1 plants. Unlike other genes responsive to SV treatment, SV-dependent decrease in FLC in wild-type plants was reversed in 35S-GSH1 plants. SV treatment increased GSSG level in wild-type seeds, whereas GSSG level was high in 35S-GSH1 plants, even at a non-vernalizing temperature. Taking into consideration that low temperatures stimulate GSH biosynthesis and bring about oxidative stress, GSSG is considered to trigger low temperature response, but enhanced GSH synthesis was not enough for mimicking SV treatment. To complete it, it essentially required the cellular redox retransition from the oxidized to the reduced state that is observed after the seed vernalization treatment. Four samples (Col-0 and 35S-GSH1 seeds imbibed at 22˚C or 4˚C). Two replicates for each samples.

2012-05-31 | E-GEOD-33978 | biostudies-arrayexpress

Transcription profiling of Arabidopsis plants with high or low ZmDREB2A expression to investigate stress responses

Project description:ZmDREB2A is a DREB2-type transcription factor cloned from maize, whose transcript was upregulated by drought, high salt, low temperature and heat stresses. The ZmDREB2A gene possesses two kinds of transcription forms by alternative splicing. Only the functional form was studied to be highly induced by stresses. Transgenic plants overexpressing ZmDREB2A (35S:ZmDREB2A) showed dwarfism and enhanced drought stress tolerance. Microarray analysis of two independent transgenic plants revealed that in addition to genes encoding LEA proteins, some genes related to heat shock and detoxification were also upregulated. Experiments on termotolerance tests of these transgenic plants showed overexpressing ZmDREB2A gene also improved plant tolerance to heat stress.

2007-04-11 | E-MEXP-819 | biostudies-arrayexpress

Effect of PCO1 overexpression [normoxia]

Project description:The effect of the overexpression of Plant Cysteine Oxidase (PCO1) on the transcriptome of Arabidopsis rosettes was investigated. For this purpose, 4-week old rosette of wild-type and 35S:FLAG:CDO1 plants were compared. Samples were composed of a pool of 5 plants. In total, 6 samples were analyzes, subdivided in 2 thesis with 3 replicates each. 35S:PCO1 plants were compared to wild-type plants.

2014-02-07 | E-GEOD-44342 | biostudies-arrayexpress

Transcriptome analysis of transgenic plants with ectopic expression (driven by 35S promoter) of At14a-Like1 (AFL1, At3g28270) YFP fusion protein.

Project description:Transcriptome analysis was used to identify genes differentially expressed in transgenic plants expressing At14a-Like1 (AFL1, At3g28270)) YFP fusion protein compared to wild type. Transcriptome analysis was performed using seedlings grown under either control conditions or low water potential stress with the objective of identifying genes associated with the increased growth caused by AFL1 overexpression under stress. The analysis identified 172 genes up-regulated and 525 genes down regulated in 35S:AFL1-YFP relative to wild type in control condtions. In the stress treatment 398 genes were up regulated and 722 down regulated in 35S:AFL1-YFP plants relative to wild type. The criteria used to identify up and down regulated genes was fold change greater than 1.5 and corrected p value M-bM-^IM-$0.05. Wild type (Col-0) or transgenic Arabidopsis thaliana seedlings were germinated on agar plates and after seven days of growth, seedlings were transferred either to fresh plates of control media or to low water potential (-1.2 MPa) stress plates. Samples were collected 10 h after transfer.

2014-10-17 | E-GEOD-62413 | biostudies-arrayexpress

Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison Total RNA was extracted from rosette leaves of two independent 3-week-old T1 Arabidopsis Col-0 plants over-expressing TaSK5 driven by 35S promoter and the whole transcriptome was compared with that of wild-type plant. Sample pairs in two independent transformants (OX7 and OX17), referred as biological replicates, were analyzed by the two-color method. Dye-swapped hybridizations were performed in every replicate.

2014-11-02 | E-GEOD-59556 | biostudies-arrayexpress

Comparison of gene expression regulated by WRKY6

Project description:WRKY6-overexpressing line 35S:WRKY6-9, knockout mutant wrky6-1 and wild-type seedlings were used to analyze genes whose expression are controlled under WRKY6. Seven-day-old seedlings of wild-type, 35S:WRKY6-9 and wrky6-1 mutant were harvested for RNA extraction.

2009-12-07 | E-GEOD-18273 | biostudies-arrayexpress

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