Comment[ArrayExpressAccession]	E-GEOD-46021
MAGE-TAB Version	1.1								
Public Release Date	2015-01-10
Investigation Title	Transcriptome analysis of in vitro MSC-derived osteoblastic cells from patients with Primary Myelofibrosis								
Comment[Submitted Name]	Transcriptome analysis of in vitro MSC-derived osteoblastic cells from patients with Primary Myelofibrosis
Experiment Description	Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm whose severity and treatment complexity is attributed to the presence of bone marrow (BM) fibrosis and alterations of stroma impairing the production of normal blood cells.  Despite the recently discovered mutations including the JAK2V617F mutation in about half of patients, the primitive event responsible for the clonal proliferation is still unknown. In the highly inflammatory context of PMF, the presence of fibrosis associated with a neo-osteogenesis and an osteosclerosis concomitant to the myeloproliferation and to the increase number of circulating hematopoietic progenitors suggests that the crosstalk between hematopoietic cells and the osteoblastic niche is deregulated in the PMF BM microenvironment. Osteoblastic niche is well known to be an important support to regulate hematopoietic stem cell functions in bone marrow. A transcriptome analysis of bone marrow mesenchymal stem cells (BM-MSC) induced in vitro to differentiate in osteoblasts will help to understand the role of these cells in pathophysiology of PMF. Transcriptome analysis was performed on BM-MSC at J0 and J21 of in vitro osteoblastic differentiation. Agilent Whole Human Genome Oligo Microarrays were used to compare expression profiling of BM-MSCs from PMF patients and healthy donors before and after osteoblastic differentiation. Primary Myelofibrosis, mesenchymal stroma cells, bone marrow, myeloproliferative disorders								
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	desterke	Martinaud	Desterke	Konopacki	Vannucchi	Guglielmelli	Boutin	Lataillade	Le Bousse-Kerdilès
Person First Name	christophe	Christophe	Christophe	Joahnna	Alessandro	Paola	Laetitia	Jean-Jacques	Marie-Caroline
Person Mid Initials					M				
Person Email	christophe.desterke@inserm.fr								
Person Affiliation	university Paris Sud11								
Person Phone	+33 (0)145595316								
Person Address	UFR medecine institute Andre Lwoff, university Paris Sud11, 14-16 avenue Paul Vaillant Couturier, VILLEJUIF, France								
Person Roles	submitter								
Protocol Name	P-GSE46021-1	P-GSE46021-5	P-GSE46021-6	P-GSE46021-2	P-GSE46021-3	P-GSE46021-4	P-GSE46021-7		
Protocol Description	the signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median ID_REF =  VALUE = Normalized signal intensity	1µg of total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technologies) following manufacturer's protocol.	The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1,65µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44k using Agilent's recommended hybridization chamber.	Bone marrow mesenchymal stromal cells induced to differentiate in osteoblastic lineage during 21 days	Mononuclear cells from human bone marrow were separate were separate by Ficoll and cultivated in medium alphaMEM with 10% of FCS and induced to differentiate in osteoblastic lineage during 21 days	RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer Platform (Agilent Technologies)	Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9,1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction.		
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 status								
Experimental Factor Type	disease status								
Comment[SecondaryAccession]	GSE46021								
Comment[GEOReleaseDate]	2015-01-10								
Comment[ArrayExpressSubmissionDate]	2013-04-12								
Comment[GEOLastUpdateDate]	2015-01-10								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-46021.sdrf.txt