"MAGE-TAB Version"	"1.1"
"Investigation Title"	"Sequencing component for the whole genome methylation analysis in PBMCs and cell subsets  pilot study"

"Experimental Design"	"cell type comparison design"	
"Experimental Design Term Source REF"	"EFO"	
"Experimental Design Term Accession Number"	"EFO_0001745"	

"Experimental Factor Name"	"cell type"	
"Experimental Factor Type"	"cell type"	
"Experimental Factor Term Source REF"	"EFO"	
"Experimental Factor Term Accession Number"	"EFO_0000324"	

"Person Last Name"	"The Wellcome Trust Sanger Institute"	
"Person First Name"	""	
"Person Mid Initials"	""	
"Person Email"	"datahose@sanger.ac.uk"	
"Person Phone"	""	
"Person Fax"	""	
"Person Affiliation"	"Wellcome Trust Sanger Institute"	
"Person Address"	"Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK"	
"Person Roles"	"submitter"	
"Person Roles Term Source REF"	""	
"Person Roles Term Accession Number"	""	

"Quality Control Type"	
"Quality Control Term Source REF"	
"Quality Control Term Accession Number"	

"Replicate Type"	
"Replicate Term Source REF"	
"Replicate Term Accession Number"	

"Normalization Type"	
"Normalization Term Source REF"	
"Normalization Term Accession Number"	

"Date of Experiment"	
"Public Release Date"	"2013-05-17"

"PubMed ID"	"24159175"	
"Publication DOI"	"10.1182/blood-2013-05-503201"	
"Publication Author List"	"Zilbauer M, Rayner TF, Clark C, Coffey AJ, Joyce CJ, Palta P, Palotie A, Lyons PA, Smith KG."	
"Publication Title"	"Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type specific hypomethylated regions."	
"Publication Status"	"published"	
"Publication Status Term Source REF"	""	
"Publication Status Term Accession Number"	""	

"Experiment 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 will be performed using two methodological approaches, the Infinium Methylation Bead Array K450 (Illumina) 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"

"Protocol Name"	"P-MTAB-32858"	"P-MTAB-32859"	
"Protocol Type"	"nucleic acid sequencing protocol"	"nucleic acid library construction protocol"	
"Protocol Term Source REF"	"EFO"	"EFO"	
"Protocol Term Accession Number"	"EFO_0004170"	"EFO_0004184"	
"Protocol Description"	"ILLUMINA sequencing using Illumina Genome Analyzer II. http://www.illumina.com/technology/sequencing_technology.ilmn"	"Libraries have been constructed from peripheral blood mononuclear cells (PBMCs) and cell subsets (CD4, CD8, CD14, CD19, CD16 and whole PBMCs) obtained from 6 healthy volunteers using Methylated DNA Immunoprecipitation Sequencing strategy (MeDIP-seq)."	
"Protocol Parameters"	""	""	
"Protocol Hardware"	"Illumina Genome Analyzer II"	""	
"Protocol Software"	""	""	
"Protocol Contact"	""	""	

"Term Source Name"	"EFO"	"NCBI Taxonomy"
"Term Source File"	"http://www.ebi.ac.uk/efo"	"http://www.ncbi.nlm.nih.gov/Taxonomy/"
"Term Source Version"	"2.34"	"2.31"

"SDRF File"	"E-ERAD-179.sdrf.txt"	
"Comment [Submitted Name]"	"Sequencing component for the whole genome methylation analysis in PBMCs and cell subsets  pilot study"
"Comment [SecondaryAccession]"	"EGAS00001000490"
"Comment [SequenceDataURI]"	"https://www.ebi.ac.uk/ega/datasets/EGAD00001000394"
"Comment [AEExperimentType]"	"methylation profiling by high throughput sequencing"
"Comment [SRASubmissionDate]"	"2013-04-22"
"Comment[ArrayExpressAccession]"	"E-ERAD-179"
"Comment [AEMINSEQEScore]"	"4"
"Comment [AEExperimentDisplayName]"	"Methylation profiling of the whole human genome in PBMCs and cell subsets using MeDIP-seq method. EGA study."