Comment[ArrayExpressAccession]	E-GEOD-71691
MAGE-TAB Version	1.1				
Public Release Date	2015-08-04
Investigation Title	Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets				
Comment[Submitted Name]	Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series				
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	Celton				
Person First Name	Magalie				
Person Email	magalie.celton@umontreal.ca				
Person Affiliation	IRIC				
Person Address	IRIC, 2950, Chemin de Polytechnique, Montreal, Quebec, Canada				
Person Roles	submitter				
Protocol Name	P-GSE71691-2	P-GSE71691-4	P-GSE71691-5	P-GSE71691-1	P-GSE71691-3
Protocol Description	Genomic DNA was isolated from the cell pellets using the PureLink Genomic DNA Mini Kit. Methyl-seq libraries were prepared for sequencing using Agilent SureSelextXT Human Methyl-seq Target enrichment system protocols	mRNA was isolated from TRIzol extraction protocol RNA libraries were prepared for sequencing using standard Illumina protocols	Human CD34+ cord blood cells were positively selected (CD34 cells)	Human CD34+ cord blood cells were positively selected (CD34 cells). Cells were transduced with a retrovirus containing GFP and the human MLL-AF9 fusion gene and were maintained for in vitro culture for 80-90 days (CD34-MLL-AF9 cells). Transduced cells were expanded in myeloid promoting culture with 15% FSC +IL3 +SCF for 4 weeks. After ~30 days of expansion cells (10 x106/mouse) from each donor sample were injected into multiple NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunodeficient mice. Mice were analyzed after ~20-24 weeks and the bone marrow was harvested (Model AML MLL_AF9 samples).	KG1a, THP-1, HL-60 and MonoMac-1 leukemia cell lines were grown in standard condition in RPMI/Opti-Media medium with 10% inactivated fetal bovine serum (FBS), penicillin (100 U/ml) and streptomycin (100 µg/ml) with 5% CO2.
Protocol Type	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol	growth protocol
Experimental Factor Name	cell line	cell subtype	cell type		
Experimental Factor Type	cell line	cell subtype	cell type		
Comment[SecondaryAccession]	GSE71691				
Comment[GEOReleaseDate]	2015-08-04				
Comment[ArrayExpressSubmissionDate]	2015-08-04				
Comment[GEOLastUpdateDate]	2015-08-07				
Comment[AEExperimentType]	methylation profiling by high throughput sequencing				
Comment[AEExperimentType]	RNA-seq of coding RNA				
SDRF File	E-GEOD-71691.sdrf.txt