Comment[ArrayExpressAccession]	E-GEOD-45000
MAGE-TAB Version	1.1					
Public Release Date	2013-08-01
Investigation Title	Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer					
Comment[Submitted Name]	Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer
Experiment Description	High-throughput analyses of concordant gene methylation and expression events were carried out for 91 human prostate specimens, including prostate cancer (T), matched normal adjacent to tumor (AT), and organ donor (OD).  Methylated DNA in genomic DNA was immunoprecipitated with anti-methylcytidine antibodies and detected by Affymetrix human whole genome SNP 6.0 chips. Methylated genomic DNA was purified by 5-hmc antibodies and Affymetrix SNP arrays were performed according to the manufacturer's manual. Copy number analysis of Affymetrix human SNP arrays was performed for both 5mc- and genomic DNA of prostate cancer samples. Methylations of genes were called when the allel amplification was reported in 5_mc DNA, and the background of the detection was suppressed by matched DNA sample. we used copy number of each probe set as baseline to detect the enrichment of methylated DNA from the same sample.  Therefore, each specimen has two arrays; one is straight copy number (*SNP.CEL), another methylation enriched DNA (*5MC_SNP.CEL). Each CNV probe is based on the design from Affymetrix but no SNP ID was assigned.					
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	Yu	Yu	Luo			
Person First Name	Yan P.	Yan	Jian-hua			
Person Mid Initials		P				
Person Email	ypyu@pitt.edu					
Person Affiliation	University of Pittsburgh					
Person Address	Pathology, University of Pittsburgh, 3550 Terrace st., Pittsburgh, PA, USA					
Person Roles	submitter					
Protocol Name	P-GSE45000-4	P-GSE45000-5	P-GSE45000-1	P-GSE45000-2	P-GSE45000-3	P-GSE45000-6
Protocol Description	As per manufacturer (Affymetrix)	DNA was restriction digested, methylated genomic DNA was immunoprecipitated and purified with 5-hmc antibody, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.	Prostate tissues were microdissected to obtain T or N samples.	Cell lines were grown according to standard conditions.	Genomic DNA was extracted from microdissected prostate tissues using Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.	The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Protocol Type	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	SAMPLE TYPE	TISSUE SUBTYPE				
Experimental Factor Type	sample type	tissue subtype				
Comment[SecondaryAccession]	GSE45000					
Comment[GEOReleaseDate]	2013-08-01					
Comment[ArrayExpressSubmissionDate]	2013-03-11					
Comment[GEOLastUpdateDate]	2013-08-03					
Comment[AEExperimentType]	methylation profiling by array					
Comment[AdditionalFile:Data1]	GSE45000_copy_number.txt					
SDRF File	E-GEOD-45000.sdrf.txt