Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human samples from the MILE (Microarray Innovations In LEukemia) study pre-phase to investigate cross site reproducibility

ABSTRACT: An international standardization program towards the application of gene expression profiling in routine leukaemia diagnostics: The MILE study pre-phase. A total of 11 laboratories from three continents performed 204 analyses using a whole-genome expression microarray. In an effort to standardize the microarray procedure, each participating centre was equipped with identical hardware, software, and reagents. Designated study operators received intensive individual training on the sample preparation protocol. Experiment Overall Design: This study is part of the MILE Study (Microarray Innovations In LEukemia) program, headed by the European Leukaemia Network (ELN) and sponsored by Roche Molecular Systems, Inc. Experiment Overall Design: Each laboratory prepared two separate cell line total RNA samples, as well as three replicate leukaemia patient lysates in two distinct project stages: (i) a five-day course of protocol training, and (ii) independent proficiency testing. Experiment Overall Design: Using unsupervised, supervised, and rÂ² correlation analyses we demonstrated that microarray analysis can be performed not only with remarkably high intra-laboratory reproducibility but also with comparable quality and reliability between eleven distinct laboratories.

ORGANISM(S): Homo sapiens

SUBMITTER: Rachel Li

PROVIDER: E-GEOD-11135 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Purpose: Aerobic capacity is a strong predictor of cardiovascular mortality. To determine the relationship between inborn aerobic capacity and soleus gene expression we examined genome-wide gene expression in soleus muscle of rats artificially selected for high and low running capacity (HCR and LCR, respectively) over 16 generations. The artificial selection of LCR caused accumulation of risk factors of cardiovascular disease similar to the metabolic syndrome seen in man, whereas HCR had markedly better cardiac function. We also studied alterations in gene expression in response to exercise training in the two groups, since accumulating evidence indicates that exercise has profound beneficial effects on the metabolic syndrome. Methods:; Soleus gene expression of both sedentary and exercise trained HCR and LCR was characterized by microarray- and gene ontology analysis. Results: Although HCR and LCR had an inborn 347% difference in running capacity, only three genes were found differentially expressed in the soleus muscle between the two groups. Up-regulation of the mitochondrial enzyme leucyl-transferRNA synthetase (LARS2) was found in the sedentary LCR. Increased expression of LARS2 has been associated with a mitochondrial DNA mutation linked to maternally inherited diabetes and mitochondrial dysfunction. In line with our findings, a growing body of evidence suggests that LCR have compromised mitochondrial function. After exercise training, 58 genes were altered in the soleus muscle of HCR, in contrast to only one in the LCR group. This suggests that animals born with different levels of fitness respond different to the same type of exercise training. Adaptations to exercise in HCR seemed to be associated with increased lipid metabolism and fatty acid elongation in the mitochondria. Also, genes associated with the peroxisomes, seemed to be central in the adaptation to exercise. Conclusion: The results indicate that (i) LCR might have mitochondrial dysfunction, which may be a contributing factor of the low inborn aerobic capacity, (ii) animals born with different levels of fitness respond different to the same exercise program. Experiment Overall Design: There are 16 samples in this study.

Dataset Information

Transcription profiling of human samples from the MILE (Microarray Innovations In LEukemia) study pre-phase to investigate cross site reproducibility

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets