Comment[ArrayExpressAccession]	E-GEOD-47817
MAGE-TAB Version	1.1			
Public Release Date	2014-04-30
Investigation Title	Epigenetic and genetic changes during mouse hematopoietic stem cell aging [RNA-Seq]			
Comment[Submitted Name]	Epigenetic and genetic changes during mouse hematopoietic stem cell aging [RNA-Seq]
Experiment Description	To investigate the global transcriptome changes in mouse hematopoietic stem cell aging, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified 4 month, and 24 month-old HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total for each age of HSC were obtained.   Comparison of the young and old HSC transcriptomes revealed that 1,337 genes that were up-regulated, and 1,297 genes were down-regulated with HSC aging. The most highly represented upstream regulator was growth factor TGFB1, accounting for ~ 19% of differential gene expression in young versus old HSC (p-value = 1.96E-33). Gene ontology (GO) analyses indicated that up-regulated genes in 24mo HSCs are highly enriched in Regulation of Cell Adhesion, Regulation of Cell Proliferation and Ribosome, while down-regulated genes are enriched in DNA Base Excision Repair, DNA replication and Cell Cycle. RNA-seq also allowed us to examine alternative isoforms with aging including alternative splicing, promoter usage and pre-mRNA abundance. Mouse hematopoietic stem cell mRNA profiles of 4 month and 24 month 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-GSE47817-4	P-GSE47817-1	P-GSE47817-3	P-GSE47817-2
Protocol Description	RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test; Genome_build: mm9 Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; deg.m04_hsc_vs_m24_hsc.txt file for two sample comparison testing if a gene is differentially expressed;	PolyA selection	Extract RNA using Qiagen Rneasy Micro kit. Tru-Seq RNA sample prep kit	Freshly forted 4 month and 24 month-old mouse HSCs (SP-KSL-CD150+)
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Comment[SecondaryAccession]	GSE47817			
Comment[GEOReleaseDate]	2014-04-30			
Comment[ArrayExpressSubmissionDate]	2013-06-11			
Comment[GEOLastUpdateDate]	2014-05-19			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AdditionalFile:Data1]	GSE47817_deg.m04_hsc_vs_m24_hsc.txt			
Comment[SecondaryAccession]	SRP025153			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR892995-SRR893002			
SDRF File	E-GEOD-47817.sdrf.txt