Comment[ArrayExpressAccession]	E-GEOD-55121
MAGE-TAB Version	1.1					
Public Release Date	2014-04-10
Investigation Title	Regulation of S-phase transcription factors by Cdk1					
Comment[Submitted Name]	Regulation of S-phase transcription factors by Cdk1
Experiment Description	Analysis of gene expression across the cell cycle from wild type cells, and cells expressing alleles of Yox1, Yhp1, Hcm1, and Tos4 that cannot be phosphorylated by Cdk1. Expression of S-phase and M/G1 transcripts are downregulated when phosphorylation of these factors is blocked, demonstrating that Cdk1 promotes expression of late cell cycle genes. These experiments are two-color hybridizations of RNA isolated from synchronized wild type (WT) or phosphomutant (4P) cells, compared to RNA from asyncrhonous wild type cells in mid-log phase. Wild type and mutant cells were synchronized in G1 phase, released into the cell cycle and samples collected at 15 minute intervals. Each time course was carried out in duplicate, the replicate experiment was performed as a dye swap.					
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	Benanti	Landry	Benanti			
Person First Name	Jennifer	Benjamin	Jennifer			
Person Mid Initials		D	A			
Person Email	Jennifer.Benanti@umassmed.edu					
Person Affiliation	University of Massachusetts Medical School					
Person Phone	508-856-1773					
Person Address	Program in Gene Function and Expression, University of Massachusetts Medical School, 364 Plantation St., LRB 525, Worcester, MA, USA					
Person Roles	submitter					
Protocol Name	P-GSE55121-1	P-GSE55121-4	P-GSE55121-5	P-GSE55121-2	P-GSE55121-3	P-GSE55121-6
Protocol Description	Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1) using default normalization settings. ID_REF =  VALUE = normalized log2 ratio (test/reference), test = synchronized WT or 4P, reference = asynchronous WT	RNA was subjected to amplification and labeling using the Agilent Low Input Quick Amp Labeling Kit protocol (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.6.pdf) with minor modifications. Briefly, cRNA was amplified by in vitro transcription with amino-allyl UTP (3:2 ratio for amino-ally UTP: UTP) overnight at 37°C. Then, cRNA was purified using RNA Clean and Concentrator columns (Zymo Research) and labeled with Cy3 or Cy5 (GE healthcare) at room temperature for 90 minutes in the dark.	600ng of each cRNA was fragmented and hybridized as per manufacturers instructions (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90050_GeneExpression_TwoColor_6.6.pdf).	Cells were arrested in G1 phase with alpha-factor for 2 hours, released from the arrest, and samples collected at 15 minute intervals.	Total RNA was extracted using an acid-phenol prep as previously described (Schmitt et al, 1990; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC330876/)	Slides were scanned on an Agilent G2505C scanner with ChipScan software version A.8.4.1.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME	GENOTYPE				
Experimental Factor Type	time	genotype				
Publication Title	Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression.					
Publication Author List	Landry BD, Mapa CE, Arsenault HE, Poti KE, Benanti JA					
PubMed ID	24714560					
Publication DOI	10.1002/embj.201386877					
Comment[SecondaryAccession]	GSE55121					
Comment[GEOReleaseDate]	2014-04-10					
Comment[ArrayExpressSubmissionDate]	2014-02-18					
Comment[GEOLastUpdateDate]	2014-04-10					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-55121.sdrf.txt