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Genome-wide CpG expression analysis of human white blood cells in obese patients under a weight loss treatment.

ABSTRACT: Genome wide expression profiling of white blood cells in obese patients under two different diets (The American Heart Association's Diet and RESMENA diet (Zulet MA et al., Nutr Hosp. 2011 Jan-Feb;26(1):16-26. )) in order to reduce weight. The Illumina HumanHT-12 v4 Expression BeadChip Kit was used, which assayed 47,000 probes.A total of 24 RNA was purified from white blood cells using a TRIZOL RNA Isolation Protocol (Life technologies) and 500 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Next, The Illumina GenomeStudio Gene Expression Software Module (v 1.9.0, Illumina, USA) was used to extract the signal intensities of each gene expression probe, which were then further preprocessed using the lumi package of Bioconductor in R. The preprocessing included background correction of the gene expression data, followed by log2-transformation and quantile normalization. It also automatically removes the control probes, leaving only the regular probes. We keep probes that are expressed in at least one individual according to a detection p-values of 5%. Assays containg SNPs within the probe were removed.

ORGANISM(S): Homo sapiens

SUBMITTER: Maria Mansego

PROVIDER: E-MTAB-2604 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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