ONTOLOGY SOURCE REFERENCE
Term Source Name	"EFO"	"NCBITaxon"	"BTO"	"SNOMEDCT"	"OMIM"	
Term Source File	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/47845"	"http://bioportal.bioontology.org/ontologies/50231"	"http://bioportal.bioontology.org/ontologies/46896"	"http://bioportal.bioontology.org/ontologies/49912"	
Term Source Version	""	"47845"	"50231"	"46896"	"49912"	
Term Source Description	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"BRENDA Tissue and Enzyme Source Ontology"	"Systematized Nomenclature of Medicine - Clinical Terms"	"Online Mendelian Inheritance in Man"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-26080"
Study Title	"Genomic DNA methylation profiling in dust-mite-allergic or aspirin-intolerant patients' CD19+ B lymphocytes. [original title: Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma.]"
Study Description	"The increase in atopic diseases has occurred in such a short period of time that it becomes difficult to be attributed only to genetic factors, which usually need more prolonged time periods to manifest. In this setting during the last decade, the science of epigenetics has increasingly developed offering new perspectives and opening a new challenging research area. In this study we aimed to study the epigenetic patterns in B CD19+ Lymphocytes from healthy and allergic patients using the improved version of HELP assay. Our study focused specifically on DNA methylation in B CD19+ Lymphocytes isolated from whole blood of dust allergic patients (ALLERGY, n=3), aspirin intolerants (ASPIRIN INTOLERANT, n=3) and healthy subjects (CONTROL, n=3). We utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI)."
Comment[Study Grant Number]	""
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Study Submission Date	""
Study Public Release Date	"2011-12-01"
Study File Name	"s_E-GEOD-26080_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"methylation profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"21975512"
Study Publication DOI	""
Study Publication Author List	"Pascual M, Suzuki M, Isidoro-Garcia M, Padr—n J, Turner T, Lorente F, D‡vila I, Greally JM"
Study Publication Title	"Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma."
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STUDY FACTORS
Study Factor Name	"patient type"	"digested"
Study Factor Type	"patient type"	"digested"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-26080_Me-Chip_assay.txt"
Study Assay Measurement Type	"DNA methylation profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE26080-1"	"P-GSE26080-6"	"P-GSE26080-5"	"P-GSE26080-2"	"P-GSE26080-8"	"P-GSE26080-3"	"P-GSE26080-4"	"P-GSE26080-7"
Study Protocol Type	"bioassay_data_transformation"	"image_aquisition"	"hybridization"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"nucleic_acid_extraction"	"labeling"	"feature_extraction"
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Study Protocol Description	"ID_REF = <br>VALUE = log2-transformed HpaII/MspI ratios"	"Scanned using a GenePix 4000B scanner (Axon Instruments) (See R.R. Selzer et al., PMID: 16075461)."	"See Roche NimbleGen website and R.R. Selzer et al., PMID: 16075461, for details."	"PBMCs were isolated using Ficoll-Paque PLUS (GE Healthcare Bio-Sciences, Sweden) and CD19+ B lymphocytes were extracted from the buffy coat using a positive immuno-magnetic separation kit (Invitrogen)"	"Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619)"	"Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619"	"Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively."	"Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as Òfailed.Ó These ÒfailedÓ loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, ÒMethylatedÓ loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either ÒmethylatedÓ or ÒfailedÓ) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (See R.F. Thompson et al., PMID: 18353789, for more details). Robust multichip average (RMA) was then applied to each group independently (See R.A. Irizarry et al., PMID: 12925520)."
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STUDY CONTACTS
Study Person Last Name	"Pascual"	"Pascual"	"Suzuki"	"Isidoro-Garcia"	"Padron"	"Turner"	"Lorente"	"Davila"	"Greally"
Study Person First Name	"Marien"	"Marien"	"Masako"	"Maria"	"Juana"	"Terrence"	"Felix"	"Ignacio"	"John"
Study Person Mid Initials	""	""	""	""	""	""	""	""	"M"
Study Person Email	"marienpdp@usal.es"	""	""	""	""	""	""	""	""
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Study Person Address	"Molecular Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA"	""	""	""	""	""	""	""	""
Study Person Affiliation	"Albert Einstein College of Medicine"	""	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""	""
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