Comment[ArrayExpressAccession]	E-GEOD-56943
MAGE-TAB Version	1.1					
Public Release Date	2014-04-22
Investigation Title	Genes regulated by Gadd45a during somatic cell reprogramming					
Comment[Submitted Name]	Genes regulated by Gadd45a during somatic cell reprogramming
Experiment Description	Gadd45a can enhance somatic cell reprogramming significantly. To explore the roles of  Gadd45a playing in reprogramming, we performed whole genome microarray to identify genes and signals pathways that regulated by Gadd45a. Genes expression of MEFs was measured at day8 in reprogramming. Three samples were set: MEFs infected with SKO plus Flag, MEFs infected with SKO plus Gadd45a and MEFs infected with SKO plus G39A which is a negative mutant of Gadd45a.					
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	Chen	Chen	Long	Liu		
Person First Name	Keshi	Keshi	Qi	Xingguo		
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science					
Person Address	Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Guangzhou, China					
Person Roles	submitter					
Protocol Name	P-GSE56943-1	P-GSE56943-4	P-GSE56943-5	P-GSE56943-2	P-GSE56943-3	P-GSE56943-6
Protocol Description	Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). ID_REF =  VALUE = Normalized signal intensity	Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).	Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。	MEFs were infected with certain virus and then cultured in DMEM/High Glucose plus +15%FBS+NEAA+Gluta Max+Sodium Pyruvate+lif for 6 days.	Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).	Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE56943					
Comment[GEOReleaseDate]	2014-04-22					
Comment[ArrayExpressSubmissionDate]	2014-04-21					
Comment[GEOLastUpdateDate]	2014-04-22					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-56943.sdrf.txt