Comment[ArrayExpressAccession]	E-GEOD-49447
MAGE-TAB Version	1.1					
Public Release Date	2013-08-02
Investigation Title	High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain					
Comment[Submitted Name]	High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain
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	Lupski					
Person First Name	James					
Person Email	jluspki@bcm.tmc.edu					
Person Affiliation	Baylor College of Medicine					
Person Address	Baylor College of Medicine, One Baylor Plaza, 604B, Houston, USA					
Person Roles	submitter					
Protocol Name	P-GSE49447-1	P-GSE49447-2	P-GSE49447-4	P-GSE49447-5	P-GSE49447-3	P-GSE49447-6
Protocol Description	Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization. ID_REF =  VALUE = normalized log10 ratio (Cy5/Cy3) representing patient/reference (chromosome X)	Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization. ID_REF =  VALUE = normalized log10 ratio (Cy5/Cy3) representing patient/reference (chromosome X 150731824-154826532)	1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37M-0C. Labeling reactions were performed according to the manufacturerM-bM-^@M-^Ys instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP, PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.	Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturerM-bM-^@M-^Ys protocol.	DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturerM-bM-^@M-^Ys protocol	Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE49447					
Comment[GEOReleaseDate]	2013-08-02					
Comment[ArrayExpressSubmissionDate]	2013-08-01					
Comment[GEOLastUpdateDate]	2013-08-04					
Comment[AEExperimentType]	comparative genomic hybridization by array					
SDRF File	E-GEOD-49447.sdrf.txt