Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Pediatric pineal germinomas: Epigenetic and genomic approach (methylation profiling)

ABSTRACT: We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. Due the low incidence of pineal germinoma, there is insufficient molecular data related to chromosomal alterations, methylation patterns and genetic expression that may help understand the changes that influence tumor development. In addition, at present, the diagnosis of this tumor in childhood is challenging because of its location and cellular origin, which is why our aim was to understand and to identify possible molecular biomarkers to provide information on the diagnosis and tumor development. Tumor biopsies were obtained from pediatric patients of 0 to 16 years of age, they were subsequently evaluated by histopathological analysis. Sample selection was based on the percentage of tumor cells present in the tumor samples, processing the samples containing the lowest 70% and 80% tumor cells, respectively.

INSTRUMENT(S): 2100 Bioanalyzer Agilent, Intel Core 2 Duo E8500 3.16 GHz or equivalent

ORGANISM(S): Homo sapiens

SUBMITTER: Normand GarcÃa HernÃ¡ndez

PROVIDER: E-MTAB-5107 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:There is growing appreciation that the feeling of well-being, alterations in mood and susceptibility to a variety of medical disorders depend on the proper expression of the master circadian clock and the synchrony among the other oscillators found in many peripheral tissues. To improve our understanding of the role of peripheral oscillators, an improved understanding of the molecular machinery sub-serving the circadian variation in gene expression is essential. Our long-term goal is to understand the molecular mechanisms that initiate circadian gene expression following external stimulation in the mammalian pineal gland. Are all or just some of the "circadian clock" genes induced by NE, cAMP, or cGMP? In this project we compare a series of gene expression patterns using DNA microarray in response to cAMP, cGMP and NE stimulation to understand why NE does not initiate circadian rhythms in the rat pineal gland. As a preliminary experiment we will compare gene expression 0, 1, and 4 h after start of chemical stimulation. A failure of NE to initiate circadian rhythms is due to failure of activation of certain "circadian clock" genes. We found that circadian rhythms are initiated by stimulation of cAMP or cGMP analogue in the rat pineal gland, while norepinephrine (NE) stimulation only moderately induce Period1 mRNA (one of "circadian clock" genes) 24 h after start of stimulation. From these results we hypothesize that external stimulation activates some "circadian clock" genes simultaneously, and that failure of circadian rhythm initiation following NE stimulation is due to insufficient "circadian clock" genes activations. Male rats of wistar strain are kept in 12h-12h light dark cycles at least for one week before start of experiments. Pineal glands are removed from animals and placed in the culture dish. Rat pineal glands are cultured for 3 days before chemical stimulation. On the day of experiment, the pineal cultures are stimulated using one of NE, cAMP and cGMP analogues for 1 or 4 h before harvest. The samples are immediately frozen and total RNA are extracted from each group which are from a pool of 8 pineal glands using Trizol reagent (Invitrogen). Concentrations of total RNA are determined using spectrophotometer, and six microgram of total RNA is aliquoted in each sample tube for further analysis. Since we already have Affymetrix Rat Genome U34A array GeneChips, we would like to send Chips as well as our total RNA samples. Experiment Overall Design: as above

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Pediatric pineal germinomas: Epigenetic and genomic approach (methylation profiling)

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