Comment[ArrayExpressAccession]	E-GEOD-42626
MAGE-TAB Version	1.1								
Public Release Date	2014-01-30
Investigation Title	Methylation profiling categorizes HIV-associated lymphomas in two distinctive groups								
Comment[Submitted Name]	Methylation profiling categorizes HIV-associated lymphomas in two distinctive groups
Experiment Description	HIV-positive patients have a higher risk of non-Hodgkin's lymphoma with poor prognostic features. To characterize features of HIV-associated lymphoma, we compared the DNA methylation profiles of 803 cancer-related genes in between 9 HIV-associated and 12 non-HIV lymphoma samples by Illumina GoldenGate Methylation Cancer Panel I microarray. Bisulfite-converted DNA from the 42 samples  (duplicate analysis of 21 samples) were analyzed to obtain the methylation profiles of cancer-associated genes by using Illumina GoldenGate Methylation Cancer Panel I microarray.								
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Matsunaga	Matsunaga	Hishima	Tanaka	Yamazaki	Motizuki	Ishizaka	Shimura	Hagiwara
Person First Name	Akihiro	Akihiro	Tsunekazu	Noriko	Maria	Makoto	Yukihito	Mari	Shotaro
Person Email	amatsunaga@ri.ncgm.go.jp								
Person Affiliation	National Center for Global Health and Medicine								
Person Phone	+81-3-3202-7181								
Person Address	Intractable Disease, National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku, Tokyo, Japan								
Person Roles	submitter								
Protocol Name	P-GSE42626-1	P-GSE42626-3	P-GSE42626-4	P-GSE42626-2	P-GSE42626-5				
Protocol Description	GenomeStudio (v2010.1) methylation module (v1.6.1) was used for dataset assembly. Data was not normalized as per manufacturer recommendation. ID_REF =  VALUE = Average Beta (not normalized) Detection Pval = 	Standard Illumina protocol	All genomic DNA was subjected to sodium bisulfite conversion, labeled with fluorescent dyes, and hybridized to GoldenGate Methylation Cancer Panel I microarray.	Genomic DNA was extracted and purified from formalin-fixed, paraffin-embedded (FFPE) by standard procedure.	Arrays were imaged using BeadArray Reader scanner using standard recommended Illumina scanner setting.				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol				
Experimental Factor Name	DISEASE STATE	AGE YRS	SEX						
Experimental Factor Type	disease state	age yrs	sex						
Publication Title	DNA methylation profiling can classify HIV-associated lymphomas.								
Publication Author List	Matsunaga A, Hishima T, Tanaka N, Yamasaki M, Yoshida L, Mochizuki M, Tanuma J, Oka S, Ishizaka Y, Shimura M, Hagiwara S								
PubMed ID	24335480								
Publication DOI	10.1097/QAD.0000000000000120								
Comment[SecondaryAccession]	GSE42626								
Comment[GEOReleaseDate]	2014-01-30								
Comment[ArrayExpressSubmissionDate]	2012-11-29								
Comment[GEOLastUpdateDate]	2014-01-30								
Comment[AEExperimentType]	methylation profiling by array								
Comment[AdditionalFile:Data1]	GSE42626_signal_intensities.txt								
SDRF File	E-GEOD-42626.sdrf.txt