Comment[ArrayExpressAccession]	E-GEOD-57151
MAGE-TAB Version	1.1																
Public Release Date	2014-04-30
Investigation Title	Epigenetic and in vivo comparison of diverse mesenchymal stromal cell sources reveals an endochonrdal signature for human hematopoietic niche formation 																
Comment[Submitted Name]	Epigenetic and in vivo comparison of diverse mesenchymal stromal cell sources reveals an endochonrdal signature for human hematopoietic niche formation 
Experiment Description	Despite similarities in morphology, phenotype and in vitro behavior, Mesenchymal Stromal Cells (MSC) form various tissue sources show striking differences in their in vivo potential to form bone, cartilage and hematopoietic support tissue.  Comparing four commonly use MSC sources (bone marrow (BM), white adipose tissue (WAT), umbilical cord (UC) and skin) we found only bone marrow (BM)-derived MSCs capable of endochondral ossification and marrow attraction. To gain mechanistic insights explaining this differences we analyzed gene expression characteristics of MSC from all four tissue sources using  Affymetrix Genechip Human Gene 2.0 ST Array. MSCs from BM, WAT, UC and skin were isolated using plastic adherence. Cells were expanded in standard alpha-MEM supplemented with pooled human platelet lysate fully replacing fetal bovine serum. MSCs were subcutaneously implanted into immune-compromised mice to comparatively evaluate bone formation and subsequent bone marrow attraction. In parallel we have isolated RNA from all sources to analyze tissue source specific gene expression profile.																
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	Reinisch	Reinisch	Etchart	Hofmann	Thomas	Fruehwirth	Sinha	Hartwig	Beham-Schmid	Trajanoski	Lin	Wagner	Dullin	Alves	Schallmoser	Andreeff	Strunk
Person First Name	Andreas	Andreas	Nathalie	Nicole	Daniel	Margareta	Subarna	Udo	Christine	Slave	Qiong	Wolfgang	Christian	Frauke	Katharina	Michael	Dirk
Person Mid Initials				A				F									
Person Email	reinisch@stanford.edu																
Person Affiliation	Stanford University																
Person Address	Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 265 Campus Drive, Stanford, CA, USA																
Person Roles	submitter																
Protocol Name	P-GSE57151-1	P-GSE57151-3	P-GSE57151-4	P-GSE57151-2	P-GSE57151-5												
Protocol Description	Arrays were normalized in R using oligolibrary. The script  (R) used  to generate the matrix is provided (data_processing_script.txt). ID_REF =  VALUE = normalized	Bioting-labeling using standard Afymetrix WT Terminal Labeling Kit	Fragmented and labeled targets were hybridized overnight at 45C, 60rpm in an Affymetrix GeneChip Hybridization Oven 645.	RNA was isolated from 5x10E6 cells using the Qiagen RNeasy PlusMini Kit.	Genechips weres scanned using the Affymetrix GeneChip Scanner 3000 7G												
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol												
Experimental Factor Name	TISSE SOURCE FOR MSCS	DONOR ID															
Experimental Factor Type	tisse source for mscs	donor id															
Comment[SecondaryAccession]	GSE57151																
Comment[GEOReleaseDate]	2014-04-30																
Comment[ArrayExpressSubmissionDate]	2014-04-29																
Comment[GEOLastUpdateDate]	2014-04-30																
Comment[AEExperimentType]	transcription profiling by array																
Comment[AdditionalFile:Data1]	GSE57151_data_processing_script.txt																
SDRF File	E-GEOD-57151.sdrf.txt