Comment[ArrayExpressAccession]	E-GEOD-45836
MAGE-TAB Version	1.1					
Public Release Date	2013-07-31
Investigation Title	Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (ChIP-chip and MIRA-chip)					
Comment[Submitted Name]	Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (ChIP-chip and MIRA-chip)
Experiment Description	To understand what dictates the emerging patterns of de novo DNA methylation, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells using MIRA-chip, ChIP-chip, and strand-specific RNA-seq, respectively. De novo methylation occurred without any apparent trigger from preexisting repressing chromatin marks but was preceded by broad, low-level transcription along the entire genome in prospermatogonia. Only distinct short sequences remained unmethylated, precisely aligned with constitutive or emerging peaks of H3K4me2. Establishment of methylation at differentially methylated regions (DMRs) of imprinted genes, CpG islands, and IAPs followed these same default rules. Transcription run-through occurred at paternal DMRs with no- or diminishing H3K4me2 peaks. Maternal DMRs remained unmethylated among highly methylated DNA at precisely aligned H3K4me2 peaks with transcription initiating at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin. ChIP-chip and MIRA-chip were performed to map histone modifications and DNA methylation at different devlopmental time points in germ cells and somatic cells along known imprinted domains and control regions, using custom NimbleGen tiling arrays.					
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	Wu	Singh	Wu	Szabo	Tran	Li
Person First Name	Xiwei	Purnima	Xiwei	Piroska	Diana	Xuejun
Person Mid Initials				E	A	
Person Email	xwu@coh.org					
Person Affiliation	City of Hope National Medical Center					
Person Address	Biomedical Informatics, City of Hope National Medical Center, 1500 E. Duarte Rd., Duarte, CA, USA					
Person Roles	submitter					
Protocol Name	P-GSE45836-1	P-GSE45836-3	P-GSE45836-4	P-GSE45836-2	P-GSE45836-5	
Protocol Description	Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction. ID_REF =  VALUE = Scaled, log2 (Cy5/Cy3) ratio	According to the standard NimbleGen protocol.	According to the NimbleGen Kit.	GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryos and fetus gonads using a MoFlo or Aria II flow cytometer. For chromatin immunoprecipitation, cells were crosslinked before sorting. Chromatin from 400,000 cells was used for one ChIP using various antibodies. For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify ChIP- and MIRA-enriched DNA.	Follow NimbleScan's default using the Agilent Scanner.	
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol	
Experimental Factor Name	MIRA	CHIP ANTIBODY	CELL TYPE	EPIGENETIC FEATURE	AGE	SEX
Experimental Factor Type	mira	chip antibody	cell type	epigenetic feature	age	sex
Publication Title	De Novo DNA Methylation in the Male Germ Line Occurs by Default but Is Excluded at Sites of H3K4 Methylation.					
Publication Author List	Singh P, Li AX, Tran DA, Oates N, Kang ER, Wu X, Szab� PE					
PubMed ID	23810559					
Publication DOI	10.1016/j.celrep.2013.06.004					
Comment[SecondaryAccession]	GSE45836					
Comment[GEOReleaseDate]	2013-07-31					
Comment[ArrayExpressSubmissionDate]	2013-04-06					
Comment[GEOLastUpdateDate]	2013-08-03					
Comment[AEExperimentType]	ChIP-chip by tiling array					
Comment[AEExperimentType]	methylation profiling by array					
SDRF File	E-GEOD-45836.sdrf.txt