Investigation Title	Transcription profiling of mouse NIH3T3 cell line cultured with and withput FGF and treated with the MEK Inhibitor U0126 at 3 time points before FGF addition reveals ERK-dependent downregulated genes have the ability to block S phase entry	
Comment[Submitted Name]	Temporal control of gene expression by ERK MAP kinase during cell cycle progression from G0/G1 to S phase	
Experimental Design	time_series_design	growth_condition_design	co-expression_design	transcription profiling by array	
Experimental Design Term Source REF	mo	mo	mo	EFO	
Comment[SecondaryAccession]	GSE4739	
Comment[ArrayExpressReleaseDate]	2007-11-24	
Comment[AEMIAMESCORE]	3	
Comment[SecondaryAccession]	GDS2124	
Comment[ArrayExpressAccession]	E-GEOD-4739	
Comment[MAGETAB TimeStamp_Version]	2010-08-05 17:24:16 Last Changed Rev: 13058	
Experimental Factor Name	Time	GrowthCondition	Compound	
Experimental Factor Type	time	growth_condition	compound	
Experimental Factor Term Source REF	
Person Last Name	Nishida	
Person First Name	Eisuke	
Person Mid Initials	
Person Email	L50174@sakura.kudpc.kyoto-u.ac.jp	
Person Phone	
Person Fax	
Person Address	Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan	
Person Affiliation	Graduate School of Biostudies, Kyoto University	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2007-11-24	
PubMed ID	16782007	
Publication DOI	16782007	
Publication Author List	Takuya Yamamoto, Miki Ebisuya, Fumito Ashida, Kazuo Okamoto, Shin Yonehara, Eisuke Nishida	
Publication Title	Continuous ERK activation downregulates antiproliferative genes throughout G1 phase to allow cell-cycle progression.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	The ERK family of MAP kinase plays a critical role in growth factor-stimulated cell cycle progression from G0/G1 to S phase. But, how sustained activation of ERK promotes G1 progression has remained unclear. Here, our systematic analysis on the temporal program of ERK-dependent gene expression shows that sustained activation of ERK is required for induction and maintenance of the decreased expression levels of a set of genes. Moreover, our cell biological analysis reveals that these ERK-dependent downregulated genes have the ability to block S phase entry. Cessation of ERK activation at mid or late G1 leads to a rapid increase of these anti-proliferative genes and results in the inhibition of S phase entry. These findings uncover an important mechanism by which the duration of ERK activation regulates cell cycle progression through dynamic changes in gene expression, and identify novel ERK target genes crucial for the regulation of cell cycle progression.	
Protocol Name	P-G4739-23	P-G4739-10	P-G4739-11	P-G4739-16	P-G4739-13	P-G4739-22	P-G4739-9	P-G4739-7	P-G4739-6	P-G4739-21	P-G4739-20	P-G4739-5	P-G4739-18	P-G4739-15	P-G4739-12	P-G4739-19	P-G4739-8	P-G4739-17	P-G4739-14	P-G4739-1	P-G4739-2	P-G4739-3	P-G4739-4	
Protocol Type	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	grow	nucleic_acid_extraction	labeling	hybridization	feature_extraction	
Protocol Description	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 7 h after stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 1 h after stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 30 min before stimulation.	NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h.	RNeasy total RNA extraction protocol (Qiagen)	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).	standard Affymetrix procedures	standard Affymetrix procedures	
Protocol Parameters	
Protocol Hardware	
Protocol Software	
Protocol Contact	
Protocol Term Source REF																							The MGED Ontology	
SDRF File	E-GEOD-4739.sdrf.txt	
Term Source Name	NCI_thesaurus	ncbitax	The MGED Ontology	ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	ncithesaurus.obo.alt	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version