Dataset Information

Ena-DATASET-DKFZ-Epigenomics-19-11-2015-09:37:32:058-207 - samples

ABSTRACT: RNA-seq of peripheral blood samples from CLL patients.

PROVIDER: EGAD00001001675 | EGA |

REPOSITORIES: EGA

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Publications

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.

Oakes Christopher C CC Claus Rainer R Gu Lei L Assenov Yassen Y Hüllein Jennifer J Zucknick Manuela M Bieg Matthias M Brocks David D Bogatyrova Olga O Schmidt Christopher R CR Rassenti Laura L Kipps Thomas J TJ Mertens Daniel D Lichter Peter P Döhner Hartmut H Stilgenbauer Stephan S Byrd John C JC Zenz Thorsten T Plass Christoph C

Cancer discovery 20131219 3

Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation hete ...[more]

PMID: 24356097

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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. Keywords: time-course

Dataset Information

Ena-DATASET-DKFZ-Epigenomics-19-11-2015-09:37:32:058-207 - samples

Publications

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.

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