Maize endosperm vp1 mutant response to water deficit
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Tim Setter
PROVIDER: E-GEOD-7672 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Due to the lack of controlled microarray experimental data, evaluation of gene identification methods has been performed using simulated data. As the ability of these approaches to mimic actual experimental data is questionable, conclusions drawn can be misleading. We applied spike-in approaches to develop experimental benchmark data and used it to evaluate various gene identification methods. mRNA that correspond to specific spots on a microarray were obtained by in-vitro transcription of selected clones. They were then spiked in at 11 varying concentrations to a common pool of mRNA, creating a set of known differentially expressed genes. mRNA was obtained from mouse ATCC CRL1606 hybridoma cells. From self hybridization results 200 genes that consistently exhibited a log ratio value close to 0 were randomly selected across a range of intensity. In-vitro transcripts of these 200 genes were obtained from their respective clones. From RNA gel electrophoresis and test array results, 169 of the 200 transcripts were deemed successful. Experiments were then conducted by spiking these 169 transcripts to the common pool of mRNA extracted from the hybridoma cells. With exception of the spiked in genes, the experimental set-up is identical to a self hybridization. This experiment is thus different from other microarray experiments as the set of differentially expressed genes is known as they have been artificially created. Spiked in genes were introduced at 11 concentrations: 0pmol (self hybridization), 0.025pmol, 0.05pmol, 0.10pmol, 0.15pmol, 0.20pmol, 0.25pmol, 0.5pmol, 0.75pmol 1pmol and 2pmol. For concentrations 0pmol, 0.05pmol, 0.10pmol, 0.25pmol, 0.50pmol and 0.75pmol, 6 replicates were obtained. For concentrations 0.025pmol, 0.15pmol, 0.20pmol, 1pmol and 2pmol, 3 replicates were obtained. Dye swaps were not performed for these experiments.
2010-06-10 | E-GEOD-2548 | biostudies-arrayexpress
Project description:Despite much knowledge is well-known on the transcriptional and enzymological regulation of many genes in starch synthesis, including SBEⅡb, Waxy, and SUS-SH1 genes, less information is available on their expression profiles as a consequence of their dysfunction. Hence, transcriptional adjustments in response to mutations were required for a better understanding of starch biosynthesis pathway, others metabolism and cell response. We used microarrays to detail the transcriptional adjustments in the endosperms of ae wx and sh1 at 15 days after pollination (DAP) compared to B73. Maize endosperms at 15 DAP were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homologic endosperms of middle ears in order to increase the temporal resolution of expression profiles.
2010-10-01 | E-GEOD-18491 | biostudies-arrayexpress
Project description:Tissue from mammary, liver, and three adipose depots (mesenteric, omental, and subcutaneous) was collected at slaughter from a cow at peak lactation to examine gene expression profiles of 7872 sequences using a bovine cDNA microarray. RNA (20 ug) from tissues and a reference standard derived from a mixture of tissues were used to make aminoallyl-labeled cDNA followed by incorporation of Cy3-ester and Cy5-ester (Amersham, Piscataway, NJ). Each experimental sample was co-hybridized with the reference standard, which allowed the treatment of fluorescence ratios as measurements of relative expression across all samples and time points. Probes were hybridized to the array for 2 days at 42 C. All samples were hybridized to duplicate slides for a total of 4 spots per cDNA element. The microarray platform has already been described [Everts et al. (2005) Vet. Immunol. Immunopathol. 105:235-245]. Slides were scanned for both dye channels with a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
2010-07-01 | E-GEOD-4495 | biostudies-arrayexpress
Project description:A series of microarray experiments by using RNA sources from UDT1-1 mutant type- and wild type-anthers at stages from meiosis to young microspore. In conjuction, microarray experiments by using RNA sources from wild type_Palea/lemmas in the flowering stage and wild type anther at pollen mitosis were performed in a time course design and compared to the microarrays of UDT1-1 mutant type- and wild type-anthers. Keywords: time-course
2010-06-09 | E-GEOD-2619 | biostudies-arrayexpress
Project description:Aneuploidy and the evolution of aneuploid karyotypes of Candida albicans strains was identified using aCGH. Whole chromosome and segmental aneuploidies, (specifically on the left arm of chromosome 5 - shown to be due to isochromosome formation) are associated with the appearance of resistance to the antifungal drug fluconazole. Keywords: Comparative Genomic Hybridization Hybridization of all strains was compared to the hybridization of SC5314, the sequenced laboratory strain.
2006-06-30 | E-GEOD-4995 | biostudies-arrayexpress
Project description:The Notch signaling is an evolutionarily conserved signal transduction cascade that plays essential roles in a variety of developmental processes. In this study, we examined the mib mutants for defects in pancreas development using in situ hybridization and GFP expression analysis of pancreas-specific GFP lines, and carried out the global gene expression profile analysis of three different mib mutantalleles. Global expression profile analysis showed that there is a significant difference in gene expression profile of wild type and three mib mutant alleles. There are 91 differentially expressed genes that are common to all three mib alleles. Through detailed analysis of microarray data we have identified several previously characterized genes and some putative Notch-responsive genes involved in pancreas development, and validated theirexpression profile using real-time PCR and in situ hybridization. We propose that this study provides a useful resource of global gene expressionprofile in mib mutants, which will be helpful in identifying the function of novel genes involved in Notch signaling and Notch-responsive genesinvolved in a variety of developmental processes. Keywords: comparison of global gene expression in mib mutant and wild type embryos All samples were analysed on Zebrafish microarray chips generated at the Genome Institute of Singapore
2010-06-25 | E-GEOD-8522 | biostudies-arrayexpress
Project description:These microarray studies were performed using whole lungs of BALB/C mice during development of hypoxia-induced pulmonary hypertension (days 1-21) and resolution of pulmonary hypertension after return to normoxia (days 22-35) . Mice were sampled during nine time-points and each time-point was replicated 4 times (with dye swapping). Keywords = hypoxia Keywords = pulmonary hypertension
2010-06-10 | E-GEOD-1909 | biostudies-arrayexpress
Project description:EKD-13 is among the recently developed mannoprotein overproducing strains. It is a recombinant derivative of the well known EC1118 commercial strain, in which the ORF of all the alleles of KNR4/SMI1 was replaced by different integration cassettes. Lack of Knr4p resulted in a negligible impairment in fermentation kinetics and a net reduction in bentonite requirements to attain complete protein stabilization of white wines made out of natural grape must. In order to improve the technological characterization of this strain, and to better understand the mechanisms underlying mannoprotein oversecretion, we have analyzed kinetics of mannoprotein release and autolysis during fermentation and aging, and we have performed a genome wide expression analysis in two different steps of the fermentation process. The results give some additional clues on KNR4 function in S. cerevisiae as well as on the best application conditions for this recombinant strain. A comparative transcriptome analysis between the S. cerevisiae recombinant strain (EKD-13) defective for KNR4/SMI1 and the wild-type strain (EC1118) was implemented. At every step of the fermentation (mid-exponential growth phase of fermentation advancement as 10 g of released CO2 and stationary-growth phase as 70 g of CO2 released) a recombinant and a WT yeast samples are put on a slide. There are three biological replicates that are labeled in dye-switch way (sometimes called biological dye-swap) for each step of fermentation leading to 3 independent intensity values for each gene (spots) on the microarrays. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology. In summary, there are six samples, each corresponding to comparisons between independent fermentations of both strains.
2011-02-28 | E-GEOD-26965 | biostudies-arrayexpress
Project description:Transcriptional analysis of stigmas was performed to identify molecules functioning in compatible pollination. Stigmas of A. thaliana Col-0 were collected (i) at 0 min or 15 min after pollination and (ii) before or at 15 min after pollen coat adhesion, and used for microarray analysis. Genes up-regulated after pollination and after pollen coat adhesion were identified. .
2014-02-26 | GSE54637 | GEO
Project description:Sexual reproduction in flowering plants involves intimate interactions between the growing pollen tube and the female reproductive structure. These interactions start immediately after pollen landing on the stigma and continue during the pollen tube journey through the style and the ovary. Thus, well before fertilization, genes in the gynoecium are affected by the growing pollen tubes. Genes activated at a distance in the ovary before pollen tubes arrival represent one class of such genes. Using a global transcriptomic approach, expression profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations revealed that these pollinations are perceived differently from a distance in the ovary. As the pollen tubes grew along the style, more and more genes became specific for each pollination type, although even early on when no difference could be observed in pollen tube growth rates, each pollination type already displayed its specific signature. Wounding experiments as well as methyl jasmonate treatment were also conducted to determine if transmitting tissue cell death caused by pollen tube growth in the style could also activate gene expression at distance in the ovary. Our data suggest that pollen tube growth in the style is at least partially perceived as a wounding aggression, and that a SI pollination is more akin to a wound response than the other pollination type tested, suggesting similarities in the signaling pathways controlling pollen recognition and stress responses. More importantly, our transcriptomic analysis reveals a highly specific recognition of various pollination types that is relayed from a distance to the ovary ahead of fertilization.
2010-05-26 | GSE21957 | GEO