ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"CL"	"BTO"	"NCBITAXON"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/CL"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	
Term Source Version	"78"	"111"	"43"	"20"	"2"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"Cell Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-19773"
Study Title	"Gene expression profiling in several types of stem cells; some cells treated with indomethacin in differentiation medium. [original title: DNA methylation in progenitor cells: expression study]"
Study Description	"Gene expression profiling of adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs). APCs were profiled either as primary cultures or after being induced to differentiate by adding indomethacin, insulin, dexamethasone, and IBMX to their growth medium. 11 samples, including 2 each of differentiated and undifferentiated ASCs. [original description: We surveyed DNA methylation profiles of all human RefSeq promoters in relation to gene expression and differentiation in adipose tissue, bone marrow and muscle mesenchymal progenitors, as well as in bone marrow-derived hematopoietic progenitors. We unravel strongly overlapping DNA methylation profiles between adipose stem cells (ASCs), bone marrow mesenchymal stem cells (BMMSCs) and muscle progenitor cells (MPCs), while hematopoietic progenitor cells (HPCs) are more epigenetically distant from MSCs seen as a whole. Differentiation resolves a fraction of methylation patterns common to MSCs, generating epigenetic divergence. RNA was isolated from MSCs isolated from various tissues and from differentiated cells, and hybridized onto Illumina expression arrays. 2-3 replicates per cell type. The supplementary file 'GSE19773_non-normalized.txt' contains the non-normalized data for Samples GSM493884-GSM493894.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2010-05-11"
Study File Name	"s_E-GEOD-19773_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"20410135"
Study Publication DOI	"10.1091/mbc.E10-01-0018"
Study Publication Author List	"S¿rensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P"
Study Publication Title	"Promoter DNA methylation patterns of differentiated cells are largely programmed at the progenitor stage."
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STUDY FACTORS
Study Factor Name	"differentiation"	"cell type"	"organism part"	"indomethacin"	"other chemicals"	"culture type"	"source tissue"	"primary culture cell type"
Study Factor Type	"differentiation"	"cell type"	"organism part"	"chemical compound"	"chemical compound"	"cell culture"	"biopsy site"	"cell type"
Study Factor Type Term Accession Number	""	""	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	"http://purl.obolibrary.org/obo/CHEBI_37577"	"http://purl.obolibrary.org/obo/BTO_0000214"	"http://www.ebi.ac.uk/efo/EFO_0000288"	"http://www.ebi.ac.uk/efo/EFO_0000324"
Study Factor Type Term Source REF	""	""	""	"EFO"	"EFO"	"BTO"	"EFO"	"EFO"
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-19773_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE19773-1"	"P-GSE19773-6"	"P-GSE19773-3"	"P-GSE19773-8"	"P-GSE19773-7"	"P-GSE19773-2"	"P-GSE19773-4"	"P-GSE19773-5"	"P-GSE19773-3a"	"P-GSE19773-3b"	"P-GSE19773-2a"	"P-GSE19773-2b"
Study Protocol Type	"bioassay_data_transformation"	"hybridization"	"grow"	"feature_extraction"	"image_aquisition"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"growth medium 1"	"growth medium 2"	"adipogenic differentiation medium"	"myogenic differentiation medium"
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Study Protocol Description	"ID_REF = <br>VALUE = Quantile-normalized signals<br>Detection_Pval = "	"Standard Illumina hybridization protocol."	"The adipose stem cells, bone marrow mesenchymal stem cells and muscle progenitor cells were cultured in DMEM/F12 Glutamax containing 10% FCS and 1% PenStrep."	"The data were quantile normalised using Illumina BeadStudio software. The non-normalized data is available in the 'GSE19773_non-normalized.txt' file, which is linked to the Series GSE19773 record as a supplementary file."	"Standard Illumina scanning protocol."	"For adipogenic differentiation, the following protocol was used: 500 ml DMEM F-12 Glutamax, 0.5 mM IBMX, 1 µM dexamethasone, 0.2 mM indomethacin, 10 µg/ ml insulin, 10 % FCS and 1 % PenStrep. For myogenic differentiation, the following protocol was used: 500 ml DMEM F-12 Glutamax, 2 % horse serum and 1 % PenStrep."	"RNA was extracted using the RNeasy Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser."	"Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit."	"ASCs and BMMSCs were grown in DMEM/F12 Glutamax containing 10% FCS and 1% PenStrep."	"MPCs were cultured in SkGM skeletal muscle medium (Lonza)."	"For adipogenic differentiation, ASCs were grown in growth medium supplemented with 0.5 mM IBMX, 1 µM dexamethasone, 0.2 mM indomethacin, and 10 µg/ ml insulin."	"For myogenic differentiation, MPCs were grown in DMEM F-12 Glutamax, 2 % horse serum and 1 % PenStrep."
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STUDY CONTACTS
Study Person Last Name	"Collas"	"Reiner"	"Jacobsen"
Study Person First Name	"Philippe"	"Andrew"	"Bente"
Study Person Mid Initials	""	"H"	"M"
Study Person Email	"geo@ncbi.nlm.nih.gov"	""	""
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Study Person Address	"Institute of Basic Medical Sciences , University of Oslo, PO Box 1112 Blindern, Oslo, Norway"	""	""
Study Person Affiliation	"University of Oslo"	""	""
Study Person Roles	"submitter"	""	""
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