Comment[ArrayExpressAccession]	E-GEOD-46888
MAGE-TAB Version	1.1						
Public Release Date	2013-10-23
Investigation Title	Comparative analysis of gene expression by human Umblical Cord (UCB)-CD34+ Hematopoietic Stem Cells (HSCs) and human induced pluripotent stem (iPS) cell-derived CD34+ Hematopoietic Progenitor Cells (HPCs)						
Comment[Submitted Name]	Comparative analysis of gene expression by human Umblical Cord (UCB)-CD34+ Hematopoietic Stem Cells (HSCs) and human induced pluripotent stem (iPS) cell-derived CD34+ Hematopoietic Progenitor Cells (HPCs)
Experiment Description	Hematopoietic stem and progenitor cells are a rare, self-renewing bone marrow resident population capable of giving rise to all circulating hematopoietic cells. They can be used therapuetically for reconstituting defective or ablated hematopoietic systems following chemotherapy, and for inducing tolerance toward allografts of the same haplotype as the HSC donor. There are several sources for HSCs, such as the adult bone marrow, or umblical cord blood, which is more replete with such HSCs. However, HSCs obtained from such sources may be immunogenic, especially if isolated from adult bone marrow. To overcome this issue, our lab has establsihed human induced pluripotent stem cell-derived HPCs with the hope of creating a nonimmunogenic, readily available and unlimited source of HSCs to use for therapy. The goal of this study was to compare the gene expression profiles of naturally found HSCs (UCB-CD34+ HSCs) and HPCs differentiated from 4 different human iPS cell lines (iPS-HPCs), so as to determine the variation between the four iPS-HPCs and whether there were any differences between these HPCs and naturally found HSCs. We utilized 4 iPS cells for this study (detailed descriptions are provided below). iPS cells were differentiated into hematopoietic progenitor cells by coculture on OP9 stromal cells, followed by enrichment of CD34+ cells through immunomagnetic bead separation. The UCB-CD34+ cells were isolated from frozen cord samples through immunomagnetic bead separation. Total RNA was isolated and human gene  Affymetrix ST 1.0 arrays performed at the University of Iowa DNA core facility. Data was analyzed, normalized and plotted on BRB Array Tools.						
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	Kim	Kim	Zavazava				
Person First Name	Eunmi	Eunmi	Nicholas				
Person Email	eunmi-kim@uiowa.edu						
Person Affiliation	University of Iowa						
Person Address	University of Iowa, 601 HWY 6 w, Iowa City, IA, USA						
Person Roles	submitter						
Protocol Name	P-GSE46888-1	P-GSE46888-5	P-GSE46888-6	P-GSE46888-2	P-GSE46888-3	P-GSE46888-4	P-GSE46888-7
Protocol Description	The data were analyzed with Heatmap.2 package using the default settings for Affymetrix analysis and normalization through global scaling. ID_REF =  VALUE = RMA normalized Intensity = Heatmap.2 package signal intensity	50ng total RNA was converted to SPIA amplified cDNA using using the WT-Ovation Pico RNA Amplification System v2 according to the manyfacturer's recommended protocol. Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module per the manufacturerM-bM-^@M-^Ys recommended protocol.	The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer, placed onto Affymetrix Human Gene 1.0 ST arrays, and incubated at 45M-: C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin, signal amplified with antistreptavidin antibody using the Affymetrix Model 450 Fluidics Station.	CD34 enriched cells were prepared for RNA extraction according to manufacturer's instructions (Qiagen's RNAeasy isolation kit).	Confluent human iPS cells were cocultured for 8-12 days on top of (70-80% confluent) OP9 stromal feeder cells in alpha MEM media supplemented with 20%FBS, 10uM ascorbic acid and 10uM MTG. The CD34+ cells were then sorted using Miltenyi CD34 beads and MACS columns according to the manufacturer's instructions.	Total RNA was performed according to the manufacturer's instructions (Qiagen's RNAeasy isolation kit).	Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	DISEASE	CELL ORIGIN					
Experimental Factor Type	disease	cell origin					
Comment[SecondaryAccession]	GSE46888						
Comment[GEOReleaseDate]	2013-10-23						
Comment[ArrayExpressSubmissionDate]	2013-05-13						
Comment[GEOLastUpdateDate]	2013-10-23						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-46888.sdrf.txt