ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"CL"	"NCBITAXON"	"PR"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/CL"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/PR"	
Term Source Version	"78"	"111"	"20"	"43"	"2"	"56"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Cell Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Protein Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-37521"
Study Title	"Dermal and adipose stem cells treated with the NSAID indomethacin and/or other drugs. [original title: RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells]"
Study Description	"Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched MSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between MSCs and FBs. A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness."
Comment[Study Grant Number]	""
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Study Public Release Date	"2012-06-27"
Study File Name	"s_E-GEOD-37521_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by high throughput sequencing"
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STUDY PUBLICATIONS
Study PubMed ID	"22723894"
Study Publication DOI	"10.1371/journal.pone.0038833"
Study Publication Author List	"JŠŠger K, Islam S, Zajac P, Linnarsson S, Neuman T"
Study Publication Title	"RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-Derived Stromal Stem Cells."
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STUDY FACTORS
Study Factor Name	"treatment"	"day"	"cell type"	"barcode"	"patient code name"	"NSAID"	"drug 1"	"drug 1 conc"	"drug 2"	"drug 2 conc"	"drug 3"	"drug 3 conc"
Study Factor Type	"treatment"	"day"	"cell type"	"barcode"	"patient code name"	"chemical compound"	"chemical compound"	"concentration"	"chemical compound"	"concentration"	"chemical compound"	"concentration"
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/CHEBI_37577"	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""
Study Factor Type Term Source REF	""	""	""	""	""	"EFO"	"EFO"	""	"EFO"	""	"EFO"	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-37521_RNA-Seq_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"nucleotide sequencing"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE37521-1"	"P-GSE37521-3"	"P-GSE37521-2"	"P-GSE37521-4"	"library construction"	"nucleic acid sequencing"	"adipogenic induction"	"osteogenic induction"	"chondrogenic induction"
Study Protocol Type	"specified_biomaterial_action"	"nucleic_acid_extraction"	"grow"	"feature_extraction"	"library construction"	"nucleic acid sequencing"	""	""	""
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Study Protocol Description	"Passage three or four cells were plated 72 hours prior to induction of differentiation. 10% FBS and 1% penicillin-streptomycin containing growth medium was supplemented with: 1 µM dexamethasone, 500 µM IBMX (3-isobutyl-1methylxanthine), 100 µM indomethacin and 10 µg/ml insulin for adipogenic induction; 100nM dexamethasone, 50 µM L-ascorbic acid 2-phosphate and 10mM glycerol 2-phosphate for osteogenic induction; 50 µM L-ascorbic acid 2-phosphate, 6,25 µg/ml insulin and 10ng/ml TGFbeta-1 (Peprotech) for chondrogenic induction."	"Total RNA was extracted using Trizol (Invitrogen). Following a phenol/chloroform extraction and isopropanol precipitation, RNA samples were treated with DNase I using DNA-free kit (Ambion). RNA-seq libraries were prepared according to the STRT protocol ("Highly multiplexed and strand-specific single-cell RNA 5' end sequencing"; Islam et al. Nature Protocols vol. 7 no. 5, 2012)"	"MSCs were isolated from human subcutaneous adipose tissue, passed through a 100 µm nylon mesh and replated in 10% FBS growth medium. After 48 h medium was replaced to remove non-adherent cells. Further cultivation was performed under standard cell culture conditions. Fibroblasts were isolated from dermal skin of the same donors as MSCs and primary culture was established by fibroblast outgrowth from skin explants placed onto Primaria dish (BD Falcon) in 10% FBS and 1% penicillin-streptomycin DMEM-High Glucose (Gibco) growth medium."	"Base-calling was performed using CASAVA on the Genome Analyzer IIx Raw reads were demultiplexed into 96 files (one per barcode, but 4 barcodes were unused) Reads were aligned using Bowtie version 0.12.7 with standard parameters Reads were then annotated using gene models obtained from UCSC on 2012-02-03. Genome_build: hg19 Supplementary_files_format_and_content: RPM (reads per million) was calculated by considering all reads mapped onto all known exons of each gene (including spliced reads) Supplementary_files_format_and_content: L127_RPM.tab (supplementary) contains a matrix of RPM values for each sample and each gene, in tab-delimited text format"	""	""	"1 µM dexamethasone, 500 µM IBMX (3-isobutyl-1methylxanthine), 100 µM indomethacin and 10 µg/ml insulin"	"100nM dexamethasone, 50 µM L-ascorbic acid 2-phosphate and 10 mM glycerol 2-phosphate"	"50 µM L-ascorbic acid 2-phosphate, 6.25 µg/ml insulin and 10 ng/ml TGFbeta-1 (Peprotech)"
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STUDY CONTACTS
Study Person Last Name	"Linnarsson"	"Jääger"	"Islam"	"Zajac"	"Linnarsson"	"Neuman"
Study Person First Name	"Sten"	"Kersti"	"Saiful"	"Pawel"	"Sten"	"Toomas"
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Study Person Email	"sten.linnarsson@ki.se"	""	""	""	""	""
Study Person Phone	"+46852487577"	""	""	""	""	""
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Study Person Address	"MBB, Karolinska Institutet, Scheeles väg 2, Stockholm, Sweden"	""	""	""	""	""
Study Person Affiliation	"Karolinska Institutet"	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""
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