E-ERAD-179 - Methylation profiling of the whole human genome in PBMCs and cell subsets using MeDIP-seq method. EGA study.

Status
Released on 17 May 2013, last updated on 10 December 2013
Organism
Homo sapiens
Samples (6)
Protocols (2)
Description
DNA methylation has been shown to play a major role in determining cellular phenotype by regulating gene expression. Moreover, dysregulation of differentially methylated genes has been implicated in disease pathogenesis of various conditions including cancer development as well as autoimmune diseases such as systemic Lupus erythematosus and rheumatoid arthritis. Evidence is rapidly accumulating for a role of DNA methylation in regulating immune responses in health and disease. However, the exact mechanisms remain unknown. The overall aim of the project is to investigate the role of epigenetic mechanisms in regulating immunity and their impact on autoimmune disease pathogenesis.The aim of this pilot study is to perform whole genome methylation analysis in peripheral blood mononuclear cells (PBMCs) and cell subsets (CD4, CD8, CD14, CD19, CD16 and whole PBMCs) obtained from 6 healthy volunteers. Whole genome methylation analysis was performed using two methodological approaches, the Illumina Infinium Methylation Bead Array K450 (see experiment E-MTAB-2145, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2145/) and MeDIP-seq. mRNA expression arrays will also be performed in order to correlate DNA methylation with gene expression as well as genotyping on the Illumina OmniExpress chip.
Experiment types
methylation profiling by high throughput sequencing, cell type comparison design
Contact
Citation
Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type specific hypomethylated regions. Zilbauer M, Rayner TF, Clark C, Coffey AJ, Joyce CJ, Palta P, Palotie A, Lyons PA, Smith KG. Blood  (2013), Europe PMC 24159175
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-ERAD-179.idf.txt
Sample and data relationshipE-ERAD-179.sdrf.txt
Links