Ena-DATASET-OSUCCC-26-09-2018-18:03:42:258-661 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004366 | EGA |
REPOSITORIES: EGA
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Project description:We analyzed the protein-coding and non-coding gene expression profiles of 64 samples of prostate cancer primary tumors. All samples were collected between 1998 and 2001 with informed consent from patients subjected to radical prostatectomy at Hospital Sirio-Libanes in São Paulo. Selected patients were identified with clinical Stage T1-2 prostate cancer and no lymph node involvement, and received no adjuvant treatment after surgery as long as they remained recurrence-free. Biochemical recurrence was defined as an increase in patient blood PSA level to 0.2 ng per mL of blood at any time during the 5-year follow-up after prostatectomy. For this kind of experiment, also called self-self hybridization, the microarrays were cohybridized with each of Cy3- and Cy5-labeled cRNA replicates. This strategy has been used to derive intensity-dependent cutoffs to classify a gene as differentially expressed or divergent in comparative genomic hybridization (CGH) studies. The comparative analysis of constant fold change cutoffs and intensity-dependent ones has been extensively discussed, showing a superior performance of the intensity-dependent strategy.
2011-06-15 | GSE18916 | GEO
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Project description:Identification of RNA–protein interactions currently requires a quantity and quality of sample that precludes their widespread application, especially for dynamic biological systems or precious samples. Here, we present Orthogonal Organic Phase Separation (OOPS), a new approach to enrich RNA Binding Proteins (RBPs) which is compatible with downstream proteomics and RNA sequencing. The flexibility of OOPS enables recovery of RBPs and free protein, or protein-bound RNA and free RNA, from a single sample in an unbiased manner. We have applied OOPS to both eukaryotic and previously inaccessible prokaryotic models, demonstrating its wide applicability, efficacy and consistency. We observe that the proteins identified include the majority of previously known RBPs, as well as novel groups of RBPs, including membrane proteins. Furthermore, applying OOPS to a cell-cycle arrest model, we can determine dynamic changes in RNA–protein interaction. Taken together, OOPS opens new model-independent, easy-to-implement opportunities to characterize RNA–protein interactions and their dynamic behaviour.
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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
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