Comment[ArrayExpressAccession]	E-GEOD-48330
MAGE-TAB Version	1.1						
Public Release Date	2013-11-05
Investigation Title	SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (U2Os cell line)						
Comment[Submitted Name]	SUMOylation Regulates the Anti-Proliferative Gene Signature Programs of Glucocorticoid Receptor (U2Os cell line)
Experiment Description	In addition to the glucocorticoids, the glucocorticoid receptor (GR) is regulated by post-translational modifications, including SUMOylation. We have analyzed how SUMOylation influences the activity of endogenous GR target genes and the receptor chromatin binding by using isogenic HEK293 cells expressing wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR). Gene expression profiling revealed that both dexamethasone up- and down-regulated genes are affected by the GR sumoylation and that the affected genes are significantly associated with pathways of cellular proliferation and survival. The GR3KR-expressing cells proliferated more rapidly and their anti-proliferative response to dexamethasone was less pronounced than in the wtGR-expressing cells. ChIP-seq analyses indicated that the SUMOylation modulates the chromatin occupancy of GR on several loci associated with cellular growth in a fashion which parallels with their differential dexamethasone-regulated expression between the two cell lines. Moreover, genome-wide SUMO-2/3 marks, which were generally associated with active chromatin, showed markedly higher overlap with the wtGR cistrome than with the GR3KR cistrome. In sum, our results indicate that the SUMOylation does not simply repress the GR activity, but regulates the activity of the receptor in a target locus selective fashion, playing an important role in controlling the GR activity on genes influencing cell growth. Total RNA isolated from U2Os cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with either vehicle (EtOH) or 100 nM of dexamethasone (dex) for 6h.						
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	Paakinaho	Paakinaho	Palvimo				
Person First Name	Ville	Ville	Jorma				
Person Mid Initials			J				
Person Email	ville.paakinaho@uef.fi						
Person Affiliation	University of Eastern Finland						
Person Address	School of Medicine/Biomedicine, University of Eastern Finland, Yliopistonranta 1E, Kuopio, Finland						
Person Roles	submitter						
Protocol Name	P-GSE48330-1	P-GSE48330-5	P-GSE48330-6	P-GSE48330-2	P-GSE48330-3	P-GSE48330-4	P-GSE48330-7
Protocol Description	Obtained data was normalized using VST transformation and RSN normalization  used as standard approach for Illumina arrays with the R/lumi package ID_REF =  VALUE = RSN normalized signal intensity Detection Pval = 	Biotinylated cRNA were prepared with the Ambion MessageAmk kit for Illumina arrays	Standart Illumina hybridization protocol	2.5x105x of U2Os cells were seeded at 6-well plates and allowed to grow in steroid-depleted medium (2.5 % charcoal stripped FBS in DMEM) 36 h and the cells were subsequently treated with 100 nM of dexamethasone for 6 h prior extraction of RNA	U2Os cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 1 mM Na-puryvate, 25 U/ml penicillin and 25 µg/ml streptomycin, and 400 µg geneticin, and kept at 37 °C in a humidified 95% air/ 5% CO2	Total RNA was extracted using TriPure (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacture's instructions	Standart Illumina scanning protocol
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	TREATMENT						
Experimental Factor Type	treatment						
Comment[SecondaryAccession]	GSE48330						
Comment[GEOReleaseDate]	2013-11-05						
Comment[ArrayExpressSubmissionDate]	2013-06-26						
Comment[GEOLastUpdateDate]	2013-11-05						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE48330_non-normalized.txt						
SDRF File	E-GEOD-48330.sdrf.txt