Comment[ArrayExpressAccession]	E-GEOD-47765
MAGE-TAB Version	1.1		
Public Release Date	2014-04-30
Investigation Title	Epigenetic changes underlying mouse hematopoietic stem cell aging		
Comment[Submitted Name]	Epigenetic changes underlying mouse hematopoietic stem cell aging
Experiment Description	We investigate the aging changes for Histone marks H3K4me3, H3K27me3 and H3K36me3 for mouse hematopoietic stem cells. Mouse hematopoietic stem cell histone methylation profiles of 4 month and 24month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000		
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	sun	Deqiang	
Person First Name	deqiang	Sun	
Person Email	deqiangs@bcm.edu		
Person Affiliation	Baylor College of Medicine		
Person Phone	7137984895		
Person Address	Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA		
Person Roles	submitter		
Protocol Name	P-GSE47765-2	P-GSE47765-1	
Protocol Description	Basecalls performed using CASAVA version 1.4 ChIP-seq reads were aligned to the mm9 genome assembly using SOAP with 2 mismatches allowed; H3K4me3 and H3K36me3 are processed by MACS and H3K27me3 are processed by SICER for peak calling genome build: mm9 processed data files format and content: BED format with 1-3 columns as chromosome, start, end. The 4th column for sicer.bed is read count. The 4th and 5th columns for peaks.bed are MACS peak id and pvalue.	Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipittaion with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	
Experimental Factor Name	CHIP ANTIBODY	IMMUNOPRECIPITATE	AGE
Experimental Factor Type	chip antibody	immunoprecipitate	age
Comment[SecondaryAccession]	GSE47765		
Comment[GEOReleaseDate]	2014-04-30		
Comment[ArrayExpressSubmissionDate]	2013-06-10		
Comment[GEOLastUpdateDate]	2014-05-19		
Comment[AEExperimentType]	ChIP-seq		
Comment[SecondaryAccession]	SRP025151		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR892966-SRR892981		
SDRF File	E-GEOD-47765.sdrf.txt