Comment[ArrayExpressAccession]	E-GEOD-45337
MAGE-TAB Version	1.1			
Public Release Date	2013-06-15
Investigation Title	Genome-wide methylation and expression analysis of two breast cancer cell lines			
Comment[Submitted Name]	Genome-wide methylation and expression analysis of two breast cancer cell lines
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series			
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	VanderKraats			
Person First Name	Nathan			
Person Email	ndvk1980@yahoo.com			
Person Affiliation	Washington University in St. Louis, School of Medicine			
Person Phone	314-362-2348			
Person Address	Center for Pharmacogenomics, Washington University in St. Louis, School of Medicine, 660 S. Euclid Ave, St. Louis, MO, USA			
Person Roles	submitter			
Protocol Name	P-GSE45337-1	P-GSE45337-4	P-GSE45337-3	P-GSE45337-2
Protocol Description	none	Genomic DNA was isolated from 3 x 10^6 cells using the Quick-gDNA MiniPrep kit from Zymo Research (Irvine, CA) according to the manufacturers instructions. The quality of the isolated high molecular weight DNA was confirmed by agarose gel electrophoresis. Methyl-MAPS libraries were prepared according to the protocol in Edwards et al Genome Research 2010. In brief, genomic DNA was split and unmethylated and methylated compartments were independently obtained by limit digestions of 10M-bM-^@M-^S15 ug of DNA with McrBC or five tetranucleotide methylation-sensitive restriction endonucleases (HpaII, HhaI, AciI, BstUI, HpyCH4IV). Digested fragments were size selected by gel-electrophoresis for fragments >800 bp. Mate-pair SOLiD sequencing libraries were then prepared using custom 6 bp barcodes. As part of the Methyl-MAPS protocol, EcoP15I CAP linkers are ligated onto the ends of the fragments. The fragments are then circularized with biotinylated internal adapters, and digested with EcoP15I, which cleaves the DNA 25-27 bp away from its recognition site. Consequently, although we sequence 35 bp for both the F3 and R3 tags, only 25 bp are guaranteed to comprise the genomic sequence tag.	Total RNA (10 ug) was isolated from MCF7 and T47D cells, DNase treated, and twice oligo(dT) selected using the Dynabeads mRNA purification kit (Invitrogen). RNA-seq libraries were constructed using the NEBNext Kit from New England Biolabs. MCF7_1 and T47D_1 libraries were constructed with custom 4 bp barcodes and sequenced with an Illumina GAIIx (32 bp single-end reads). MCF7_2 and T47D_2 libraries were constructed with standard Illumina indexed primers and sequenced using Illumina HiSeq 2000 (42 bp single-end reads).	MCF7 and T47D cell lines were maintained in RPMI 1640 medium supplemented with 5% fetal bovine serum, 10 mmol/L HEPES, 4.5 g/L glucose, 2 mmol/L L-glutamine, 1 mmol/L sodium pyruvate, and 50 M-5g/ml gentamicin in a humidified 37M-0C incubator containing 5% carbon dioxide.
Protocol Type	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	CELL LINE			
Experimental Factor Type	cell line			
Publication Title	Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes.			
Publication Author List	Vanderkraats ND, Hiken JF, Decker KF, Edwards JR			
PubMed ID	23748561			
Publication DOI	10.1093/nar/gkt482			
Comment[SecondaryAccession]	GSE45337			
Comment[GEOReleaseDate]	2013-06-15			
Comment[ArrayExpressSubmissionDate]	2013-03-20			
Comment[GEOLastUpdateDate]	2013-06-21			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AEExperimentType]	methylation profiling by high throughput sequencing			
SDRF File	E-GEOD-45337.sdrf.txt