Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of an Arabidopsis thaliana mutant deficient in the GAPC gene.

ABSTRACT: To investigate the role of this enzyme in different plant tissues, we characterized a mutant from Arabidopsis thaliana having an insertion at the GAPC gene locus. The homozygous mutant was determined to be null respect to GAPC, as it exhibited complete absence of both expression of GAPC mRNA and enzyme activity. Transcriptome analysis demonstrated that the insertion mutant plant shows altered expression of several enzymes involved in carbohydrate metabolism. Keywords: 2 channel experiment in triplicate including a dye swap comparison

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE3540 | GEO | 2006/10/31

SECONDARY ACCESSION(S): PRJNA93601

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.

Project description:Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) is a conserved protein found in higher plants. In photosynthetic cells, the enzyme is involved in a shuttle transfer mechanism to export NADPH from the chloroplast to the cytosol. In this work, we demonstrate that GAPN gene express in leaves and roots at similar levels; showing the highest level of expression in flowers. To investigate the role of this enzyme in different plant tissues, we characterized a mutant from Arabidopsis thaliana having an insertion at the GAPN gene locus. The homozygous mutant was determined to be null respect to GAPN, as it exhibited complete absence of both expression of GAPN mRNA and enzyme activity. Transcriptome analysis demonstrated that the insertion mutant plant shows altered expression of several enzymes involved in carbohydrate metabolism. Significantly, cytosolic phosphorylating (NAD-dependent) glyceraldehyde-3-phosphate dehydrogenase mRNA levels are induced in the mutant, which correlates with an increase in enzyme activity. mRNA levels and enzymatic activity of glucose-6-phosphate dehydrogenase were also elevated, correlating with an increase in NADPH concentration. Moreover, an increased levels of oxidative stress was measured in the mutant plants. Downregulation of several glycolytic and photosynthetic genes suggests that GAPN is important for the efficiency of both metabolic processes. The results presented demonstrate that GAPN has a relevant role in plant growth and development. Keywords: 2 color experiment in triplicate including dye-swap

2005-11-23 | GSE3539 | GEO

Expression profiling of Ruminococcus flavefaciens FD-1 with growth on cellulose or cellobiose

Project description:This study compares growth of Ruminococcus flavefaciens FD-1 with cellulose or cellobiose as the carbohydrate substrate. Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application to improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. These results show that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components. 1 species (Ruminococcus flavefaciens FD_1), 2 conditions (cellulose, cellobiose), 4 biological replicates. Direct design with biological dye swap.

2010-05-16 | E-GEOD-15916 | biostudies-arrayexpress

Midgut gene expression after induction by 11 compounds

Project description:Midgut gene expression after induction by 11 compounds: each treatment was done in biological triplicate and using dye swap resulting in 6 microarrays per treatment. on each microarray a treated midgut RNA was compared to a DMSO treated midgut RNA. indole3carbinol, xanthotoxine, 2tridecanone, clofibrate, indole, phenobarbital, quercetine, methoprene, methoxyfenozide, deltamethrine and fipronil

2018-09-22 | GSE32368 | GEO

Screening for candidate clock-controlled genes

Project description:Microarrays were hybridized with a mixture of solutions containing LL2 cDNA labeled with Cy3 or Cy5 (dye-swap) and LL14 cDNA labeled with Cy5 or Cy3 (dye-swap). Keywords: repeat sample

2004-12-29 | GSE2114 | GEO

Time course effect of A-factor addition

Project description:Comparative hybridization of afsA deficient mutant versus afsA deficient mutant after A-factor addition 3 x dual channel slides, dye swap

2010-06-24 | E-GEOD-13804 | biostudies-arrayexpress

Effect of AdpA deficient

Project description:Comparative hybridization of wild type versus AdpA deficient mutant 4 x dual channel slides, dye swap

2010-05-26 | E-GEOD-9882 | biostudies-arrayexpress

BYxwild_40

Project description:Expression analysis of F1 haploid segregants from a cross between BY4716 (isogenic to S288c) and a wild isolate collected by R. Mortimer. Each segregant sample was subjected to a dye-swap pair of arrays. All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent segregants. All sample titles are of the form S1-S2. S1 indicates the sample whose signal was read as channel 1 (Cy5 labeling, fluorescence at 635 nm) and S2 as channel 2 (Cy3, 532 nm). Keywords: repeat sample

2002-05-01 | GSE37 | GEO

Effect of AdpA deficiency on S. griseus cells grown in SMM medium

Project description:Comparative hybridization of wild type versus AdpA deficient mutant grown on SMM medium 3 x dual channel slides, dye swap

2010-05-22 | E-GEOD-14770 | biostudies-arrayexpress

Kidney development time course

Project description:Array Design; Mouse Compugen 22K Spotted Oligo Author; Sean Grimmond Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene) Concentration; 100 Data processing/normalization; Lowess Normalisation GeneSpring) Developmental Stage; embryonic Diseased/Normal; normal Dye Swap; red/green Experiment Type; time course Genetic Characteristic; Wild type Image Analysis Software; Imagene5.5 (Biodiscovery) Labeling Protocol; Amino Allyl Message Amp- Ambion Organ/Organism part; kidney Organism; Mus Musculus RNA type; aRNA Message Amp-ambion Tissue Type; Pool of whole organs Organization; IMB, Uni of QLD, Brisbane Australia Sample Source; primary tissue Sampling Method; Dissection of whole organ Sex; Pool of both sexes Strain/Cell-line; CD1 Series_overall_design: To account for dye swap, the signal channel and control channel measurements for each sample were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Specific samples were normalized to one another: sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples. Keywords: time-course

2005-07-20 | GSE2282 | GEO

DNA methylation in wild-type bolting Arabidopsis thaliana plants

Project description:The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype. McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment. In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. The two samples in this series are complementary hybridizations in a dye-swap analysis. This is the normalized result of the paired dye swap samples VC121 and VC127. The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. These samples were not subjected to hypothesis testing. Therefore, P-values are reported as -1 and no features are flagged as significantly methylated. Keywords: other

2004-06-12 | GSE1329 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data