Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rat small and large retinal ganglion cells

ABSTRACT: Different sub-types of ganglion cells existing in mammalian retinas possessing distinct function in processing the visual information. In primates, RGC are commonly divided into midget cells, which are relatively small, and parasol cells, with a larger soma size. Rodents also possess morphologically distinct populations, but their physiological properties are less characterized. The two types of mammalian RGCs differ in their response to pathological conditions such as retinal ischemia, diabetic retinopathy and glaucoma. In this work, we compared gene expression profiles of large (LRGCs) and small (SRGCs) ganglion cells isolated from rat retina in attempt to identify molecular determinants underlying differences in function and tolerance to stress. Experiment Overall Design: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the SRGC and LRGC sub-populations. Actinomycin D was added to prevent new transcription during experimental procedures. Purified cells were used for RNA isolation. Following two rounds of linear amplification aRNA probes were hybridized with two-color Agilent Rat Genomic Oligo Arrays. We utilized the dye swap experimental design to eliminate the dye bias effects and make data from different experiments available for the cross-comparison.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Dmitry Ivanov

PROVIDER: E-GEOD-11468 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We used gene microarray analysis to compare the global expression profile of genes involved in adaptation to exercise training in skeletal muscle from chronically strength/resistance trained (ST), endurance trained (ET) and untrained control subjects (Con). Resting skeletal muscle samples (~100mg) were obtained from the vastus lateralis of 20 subjects (Con n=7, ET n=7, ST n=6; trained groups >8 years specific training). Total RNA was extracted from tissue and microarrays completed, with test samples compared with standard human reference RNA. Subjects were characterised by performance measures of maximal oxygen uptake (VO2max) on a cycle ergometer and maximal concentric and eccentric leg strength on an isokinetic dynamometer. 263 genes were differentially expressed in trained (TR collectively ET + ST) subjects compared with Con (P<0.05) while 21 genes were different between ST and ET (P<0.05). Manual cluster analyses revealed significant regulation of genes involved in muscle structure and development in TR subjects compared with Con (P<0.05), and expression of these correlated significantly with measures of performance (P<0.05). ET had increased and ST decreased expression of gene clusters related to mitochondrial/oxidative capacity (P<0.05), and these mitochondrial gene clusters correlated significantly with VO2max (P<0.05). VO2max also correlated with expression of gene clusters that regulate fat and carbohydrate oxidation (P<0.05). We have demonstrated that chronic training has marked effects on basal gene expression by regulating levels of multiple mRNAs that transcribe genes for important functional groups in human skeletal muscle. Some specific gene clusters are expressed regardless of the training stimulus, whereas others exhibit divergent expression patterns as a result of specific training stimuli. Keywords: Comparative, cluster analysis, endurance training, strength training, muscle phenotype This was a crossectional study examining basal gene expression profiles of the human vastus lateralis. Twenty healthy males volunteered for this investigation. Seven were endurance trained cyclists (ET), who had been participating in endurance training for 8 yr. These subjects had no history of resistance training. Six subjects were strength trained power-lifters (ST) who had been participating exclusively in strength/resistance training for 9 yr. The final seven subjects were healthy controls (CON) that did not participate in any formal exercise. The study was approved by the Human Research Ethics Committee of RMIT University and Monash University Standing Committee on Ethics Research on Humans. After RNA extraction, amplification and indirect labelling, a dual colour micro-array analysis was conducted by hybridizing a test (muscle RNA; Cy5) sample and a reference (Universal human RNA; Cy3) sample on the AGRF glass slide human 8K micro-array. After data capture with the Genepix scanner and associated software data was normalised and the three populations compared using GeneSpring and simplified cluster analysis.

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Transcription profiling of rat small and large retinal ganglion cells

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