Comment[ArrayExpressAccession]	E-GEOD-43059
MAGE-TAB Version	1.1						
Public Release Date	2013-12-01
Investigation Title	Role of Jmjd2b and Jmjd2c in mESCs identity						
Comment[Submitted Name]	Role of Jmjd2b and Jmjd2c in mESCs identity
Experiment Description	We used microarray to determine the changes in gene expression profile after KD of Jmjd2b and Jmjd2c compared to Anti-GFP KD from mES cells Mouse ES cells were infected with AntiGFP, Jmjd2b and Jmjd2c shRNAs lentivirus, puromycin selected, passage them 2-3 times, collected for RNA isolation and gene expression						
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	Shao	Das	Shao	Orkin			
Person First Name	Zhen	Partha	Zhen	Stuart			
Person Mid Initials		P		H			
Person Email	shao@bloodgroup.tch.harvard.edu						
Person Affiliation	Dana Farber Cancer Institute and  	Children's Hospital Boston						
Person Address	Hematology/Oncology, Dana Farber Cancer Institute and  	Children's Hospital Boston, 1 Blackfan Circle, Karp Research Building 07007F, Boston, MA, USA						
Person Roles	submitter						
Protocol Name	P-GSE43059-1	P-GSE43059-5	P-GSE43059-6	P-GSE43059-2	P-GSE43059-3	P-GSE43059-4	P-GSE43059-7
Protocol Description	The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness. ID_REF =  VALUE = Model-based expression value by dchip.	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	mESCs were collected through trypsinization, washed with PBS twice, followed by RNA extraction	mESCs were grown in standard mouse ES cells media with LIF	Total RNA was extracted using RNAeasy plus mini kit according to the manufacturer's instructions.	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
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	GENOTYPE						
Experimental Factor Type	genotype						
Comment[SecondaryAccession]	GSE43059						
Comment[GEOReleaseDate]	2013-12-01						
Comment[ArrayExpressSubmissionDate]	2012-12-20						
Comment[GEOLastUpdateDate]	2013-12-01						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-43059.sdrf.txt