Investigation Title Transcription profiling of human bone marrow and adipose tissue-derived stromal cells Comment[Submitted Name] Molecular profiling of human bone marrow and adipose tissue-derived stromal cells Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] GSE8954 Comment[ArrayExpressReleaseDate] 2009-01-13 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-8954 Comment[MAGETAB TimeStamp_Version] 2010-08-09 12:01:45 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Saulnier Person First Name Nathalie Person Mid Initials Person Email nathalie.saulnier@rm.unicatt.it Person Phone Person Fax Person Address Università Cattolica del Sacro Cuore di Roma, Largo Francesco Vito,1, Roma, 00168, Italy Person Affiliation Università Cattolica del Sacro Cuore di Roma Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-01-13 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood. The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.We identified an overlapping dataset of 190 genes commonly regulated by ATSC and BMSC. Among these, we were able to categorize 6 key biological families that could be regarded as a stemness signature that underlie the self-renewal potential and the ability to generate progenitor cells. In particular, a pivotal role of signalling pathways along with the expression of numerous transcription regulators emerged from this study. Genes specifically modulated in ATSC, suggested that these cells posses anti-oxidative and neuroprotective properties. Taken together, these results provide new hints towards the understanding of the molecular basis of MSC maintenance and suggest that ATSC have interesting properties which could be useful for several potential clinical applications. Experiment Overall Design: Bone marrow and adipose tissue samples were respectively obtained from four long-term disease-free Hodgkin lymphoma patients, during follow-up investigation and from four patients subjected to partial abdominoplasty. In addition, we used in this study a cell line (MRC-5 cells) as control to rule out genes involved in homeostasis and emphasize genes specifically expressed in both types of mesenchymal stem cells. To have results statistically significant, we enrolled four patients for each tissue (4 chips/tissue) and we performed a technical replicate (triplicate) for the MRC-5 cells. Protocol Name P-G8954-1 P-G8954-5 P-G8954-3 P-G8954-4 P-G8954-6 P-G8954-2 P-AFFY-6 Affymetrix:Protocol:ExpressionStat Protocol Type grow grow nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction labeling feature_extraction bioassay_data_transformation Protocol Description Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.) Cells were grown in DMEM additioned with 10% fetal bovine serum (FBS) and 1% of antibiotics. Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel. Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel. Total RNA from 1 million of MRC-5 cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel. Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.) Title: Affymetrix CEL analysis. Description: Title: Affymetrix CHP Analysis (ExpressionStat). Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF The MGED Ontology SDRF File E-GEOD-8954.sdrf.txt Term Source Name ncbitax The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version