Project description:Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons. Keywords: other
Project description:gnp06-01_agriarray - multiplexage : dual-target hybridization microarray experiment - Several factors affect today a more extended use of microarrays for research and as a diagnosis tool. These factors are the experimental cost, the reproducibility of the measurements and the format of the analyses. This project aims at bringing solutions in these three domains by optimizing multiplexed analyses in order to reduce cost and enhance the number of samples treated simultaneously; by proposing new couples flurophores / slide surface in order to increase the signal precision and by developing new applications such as Comparative Genomic Hybridization (GGH) or Promoter Arrays to bring the plant microarray beyond transcriptome analyses. Altogether, these approaches will allow us to construct an optimized diagnostic tool based on 96 well microplate microarrays. This multidisciplinary project bring together biologists, chemists, physicists and mathematicians to develop innovative solutions for future application of DNA microarrays. - Dual-target hybridization microarray experiment with doble factors comparison : two mutants and its wild-types at different times. The aim of this part is to compare the classical design with the new design with a third dye.
Project description:Comparative genomic hybridization analysis for detection of recurring gene copy number variation (CNV) among a set of lung cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled Agilent characterized normal human reference DNA
Project description:Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons.
Project description:Hybrid matings between A. thaliana and A. arenosa result in post zygotic seed lethality resulting in hybridization barrier between the two species. This barrier can be overcome to a large degree by increasing the genome dosage of the maternal genome (i.e. A. thaliana) in a cross between the two species. In this experiment we assayed the transcriptome of an incompatible cross (2x At x 2x Aa) with high seed lethality and a compatible cross (4x At x 2x Aa) using silique tissue at 5 days after pollination. We used microarrays to identify dosage responsive gene in interspecies hybridization Keywords: differential expression
Project description:The Males Experiment: This experiment was done to test the sensitivity of our array in detecting single copy losses of probes to the X chromosome. Males (XO) have just one X chromosome, while hermaphrodites (XX) have two. CB4856 and JU258: This experiment was done to determine the natural copy number variation that exists in a wild C. elegans isolate. Extensive natural copy number variation exists in this strain. gkDf2 (VC100): This control experiment was done to confirm that we could reliably detect a large 50-kb homozygous deletion on chromosome X using this array. gk329 (VC766): This control experiment was done to confirm that we could reliably detect a homozygous 1-kb single-gene deletion on the X chromosome. This deletion targets the gene ceh-39. For gk291 (VC615): This control experiment was done to confirm that we could reliably detect a heterozygous (single copy) single-gene 1-kb deletion on chromsome II. This deletion targets the gene dab-1. All other experiments: This experiment was done in an effort to detect novel balanced single copy losses on chromosome II in mutagenized strains. Mutants were previously screened for homozygous lethal mutations on chromosome II, and these mutations were then balanced with the mIn1 balancer chromosome to generate the mutant strain screened in this experiment. Keywords: comparative genomic hybridization