Comment[ArrayExpressAccession]	E-GEOD-44776
MAGE-TAB Version	1.1					
Public Release Date	2013-10-31
Investigation Title	DamID for MBD3 in human breast cancer cell lines					
Comment[Submitted Name]	DamID for MBD3 in human 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	Mav					
Person First Name	Deepak					
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	SRA International, Inc					
Person Address	SRA International, Inc, 2605 Meridian Pkwy, Suite 200, Durham, NC, USA					
Person Roles	submitter					
Protocol Name	P-GSE44776-1	P-GSE44776-4	P-GSE44776-5	P-GSE44776-2	P-GSE44776-3	P-GSE44776-6
Protocol Description	The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. The normalized values presented here are the residuals obtained from loess regression (log2(cy5) was treated as dependent and log2(cy3) as explanatory variables) for CG count bin. These approach is similar to localized MA loess normalization the difference being that instead of predicting M (log2(Cy5/cy3)) using A (log2(cy5*cy3)) locally (using subset of probes) we attempt to predict log2(cy5) using log2(cy3) using probes that are similar in terms of their CG count. The multiple signal values from same probe within array were averaged. Furthermore, the resulting signal values for MIRA and ChIP-antibody samples were quantile normalized independently to adjust for between sample variations. ID_REF =  VALUE = normalized log2 ratio (Cy5/Cy3)	1ug DNA was labeled with Nimblegen Dual-Color DNA labeling kit followed by NimbleGen Arrays User's Guide (version 6.2)	Hybridizaion was performed followed by NimbleGen Arrays User's Guide (version 6.2)	Cells were cultured with DMEM/F12 supplemented with 10% fetal bovine serum	Genomic DNA was purified and processed for DamID as described in Nature Protocol 2007;2(6):1467-78.	Scanning was performed as described in Lai AY et al. (J Exp Med. 2010 Aug 30;207(9):1939-50)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL LINE	REPLICATE	FRACTION			
Experimental Factor Type	cell line	replicate	fraction			
Comment[SecondaryAccession]	GSE44776					
Comment[GEOReleaseDate]	2013-10-31					
Comment[ArrayExpressSubmissionDate]	2013-03-01					
Comment[GEOLastUpdateDate]	2013-11-03					
Comment[AEExperimentType]	ChIP-chip by tiling array					
SDRF File	E-GEOD-44776.sdrf.txt