Comment[ArrayExpressAccession]	E-GEOD-45460
MAGE-TAB Version	1.1						
Public Release Date	2013-03-26
Investigation Title	Expression data from early human B-cell development						
Comment[Submitted Name]	Expression data from early human B-cell development
Experiment Description	A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res. 2012 Dec;40(22):11339-51. We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays. We identified a distinct development-dependent demethylation signature which has gene expression regulatory properties for pre-B cells, and provide a catalog reference for the epigenetic changes that occur in pre-B-cell leukemia and other B-cell-related diseases. Human fetal bone marrow was obtained, and using flow cytometry antibodies, four populations of B-cell developmental stages including stage 1 (S1; predominantly multipotent progenitors before lineage commitment and common lymphoid progenitors), stage II (S2; pre-B-I cells), stage 3 (S3; pre-B-II cells) and stage 4 cells (S4; immature B cells). For 8 indibiduals, DNAs and RNAs were isolated and the methylation and expression changes during early B-cell development were identified using the Illumina HumanMethylation450 Beadchip (Illumina) and GeneChip Human Gene 1.0 ST Array (Affymetrix).						
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	Lee	Lee	Xiao	Wiemels			
Person First Name	Seung-Tae	Seung-Tae	Yuanyuan	Joseph			
Person Mid Initials				L			
Person Email	essere2@naver.com						
Person Affiliation	Samsung Medical Center						
Person Phone	+82-2-3410-2710						
Person Fax	+82-2-3410-2719						
Person Address	Laboratory Medicine & Genetics, Samsung Medical Center, 50 Iron-Dong KanangmGu, Seoul, - None -, South Korea						
Person Roles	submitter						
Protocol Name	P-GSE45460-1	P-GSE45460-6	P-GSE45460-5	P-GSE45460-2	P-GSE45460-3	P-GSE45460-4	P-GSE45460-7
Protocol Description	ID_REF =  VALUE = RMA normalized signal intensity	GeneChips were scanned using the Affymetrix genechip scanner	Following fragmentation, cRNA were hybridized onto GeneChip Human Gene 1.0 ST Array (Affymetrix) according to Affymetrix's instructions.	Four stages of B-cell precursors were isolated via flow cytometry sorting	AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions	1 μg of high-quality total RNA was amplified and labeled (NuGen Ovation)	Data was processed and normalized using the Expression Console software (Affymetrix) with the standard Robust Multi-array Average (RMA) algorithm
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	CELL TYPE						
Experimental Factor Type	cell type						
Publication Title	A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network.						
Publication Author List	Lee ST, Xiao Y, Muench MO, Xiao J, Fomin ME, Wiencke JK, Zheng S, Dou X, de Smith A, Chokkalingam A, Buffler P, Ma X, Wiemels JL						
PubMed ID	23074194						
Publication DOI	10.1093/nar/gks957						
Comment[SecondaryAccession]	GSE45460						
Comment[GEOReleaseDate]	2013-03-26						
Comment[ArrayExpressSubmissionDate]	2013-03-24						
Comment[GEOLastUpdateDate]	2013-03-26						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-45460.sdrf.txt