Comment[ArrayExpressAccession]	E-GEOD-37315
MAGE-TAB Version	1.1					
Public Release Date	2014-04-24
Investigation Title	Murine bone marrow cells: Wild-type vs. PU.1 knockdown					
Comment[Submitted Name]	Murine bone marrow cells: Wild-type vs. PU.1 knockdown
Experiment Description	Genome-wide screen for aberrant DNA methylation in bone marrow of PU.1 knockdown mice compared to control wildtype animals in three stages 7 age and gender matched mice pairs in the preleukemic stage, 5 pairs in the early leukemic stage and 7 pairs in the late leukemic stage					
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	Sonnet	Claus	Sonnet			
Person First Name	Miriam	Rainer	Miriam			
Person Email	M.Sonnet@dkfz-heidelberg.de					
Person Affiliation	German Cancer Research Center					
Person Address	German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany					
Person Roles	submitter					
Protocol Name	P-GSE37315-1	P-GSE37315-4	P-GSE37315-5	P-GSE37315-2	P-GSE37315-3	P-GSE37315-6
Protocol Description	Data from arrays were extracted with the Agilent Feature extraction software, background-corrected with the NormExp method (offset 50) and within-array-normalised with a rank-invariant loess regression method. ID_REF =  VALUE = normalized log2 ratio (Alexa5/Alexa3) representing test/reference	Enriched highly methylated DNA (approx. 30 ng) was labeled in a 50 µl reaction mix (Invitrogen, BioPrime Total Genomic Labeling System) with either Alexa 5 (PU.1 knockdown animals) or Alexa 3 (wildtype animals) and subsequently purified using the BioPrime Purification Module	Differentially labeled DNA samples from age and gender matched animals were pooled and hybridized with the Agilent aCGH Hybridization Kit to Agilent mouse CpG island tiling arrays according to the manufacturer´s instructions	Heterozygous mice were bred to obtain homozygous wildtype and knockdown littermates	DNA was extracted using the Qiagen AllPrep kit following the manufacturer´s instructions. Highly methylated DNA was enriched using methyl-CpG immunoprecipitation according to Gebhard et al., Cancer Res. 2006.	Scanned on an Agilent G2565CA scanner. Agilent Feature Extraction Software (v 8.5.1.1)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DISEASE STATE	AGE				
Experimental Factor Type	disease state	age				
Comment[SecondaryAccession]	GSE37315					
Comment[GEOReleaseDate]	2014-04-24					
Comment[ArrayExpressSubmissionDate]	2012-04-16					
Comment[GEOLastUpdateDate]	2014-04-24					
Comment[AEExperimentType]	methylation profiling by array					
SDRF File	E-GEOD-37315.sdrf.txt