Comment[ArrayExpressAccession]	E-GEOD-54741
MAGE-TAB Version	1.1						
Public Release Date	2014-04-03
Investigation Title	Microarray analysis comparing yeast Eco1 mutant W216G to mutants of FOB1 and RAD61						
Comment[Submitted Name]	Microarray analysis comparing yeast Eco1 mutant W216G to mutants of FOB1 and RAD61
Experiment Description	Eco1 is an acetyltransferase subunit of the cohesin complex and acts during DNA replication to establish cohesion between sister chromatids. However, cohesin has additional functions in gene expression, DNA damage repair, and higher-order organization of chromosomes. The eco1 mutant W216G disrupts acetyltansferase activity, and causes genome-wide transcriptional defects which can be suppressed by deletion of FOB1, a gene also involved in DNA replication. This experiment investigates gene expression differences between the eco1-W216G mutant, and mutants in FOB1, and RAD61 a gene involved in inhibition of cohesion establishment but mutation of which is able to suppress temperature sensitivity of the eco1-W216G mutant. Wt and mutant strains of yeast were grown to mid log phase in liquid culture in triplicate and harvested for comparison on Affymetrix microarrays. The following strains were compared: 1) eco1-W216G, 2) eco1-W216G fob1Δ, 3) eco1-W216G rad61Δ, 4) fob1Δ, 5) rad61Δ, and 6) WT.						
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	Seidel	Lu	Xiong	Seidel	Gerton		
Person First Name	Chris	Shuai	Bo	Chris	Jennifer		
Person Mid Initials	W			W	L		
Person Email	seidel@phageT4.org						
Person Affiliation	Stowers Institute						
Person Phone	816 926 9054						
Person Address	Genomics, Stowers Institute, 1000 E 50th St, Kansas City, MO, USA						
Person Roles	submitter						
Protocol Name	P-GSE54741-1	P-GSE54741-5	P-GSE54741-6	P-GSE54741-2	P-GSE54741-3	P-GSE54741-4	P-GSE54741-7
Protocol Description	The Affymetrix Yeast Genome 2.0 array contains probes designed for both S. pombe and S. cerevisiae. Data from the arrays was filtered to exclude probes annotated to S. pombe, and retain those annotated to S. cerevisiae genes. Array intensities were processed using the RMA algorithm in the affy library (version affy_1.36.1) from bioconductor in R version 2.15.2. ID_REF =  VALUE = Normalized linear array intensity.	Biotinylated cRNA was prepared from 300 ng Total RNA using MessageAmp III aRNA Kit from Ambion.	Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	Cells growing in exponential phase in YPD+CSM were pelleted by centrifugation.	Cultures were innoculated from fresh overnights and grown at 30C in YPD+CSM to an OD as indicated.	Total RNA was extracted using the hot acid phenol method.	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	EXPERIMENT_DATE	STRAIN_ID	REPLICATE	GENOTYPE			
Experimental Factor Type	experiment_date	strain_id	replicate	genotype			
Publication Title	The cohesin acetyltransferase Eco1 coordinates rDNA replication and transcription.						
Publication Author List	Lu S, Lee KK, Harris B, Xiong B, Bose T, Saraf A, Hattem G, Florens L, Seidel C, Gerton JL						
PubMed ID	24631914						
Publication DOI	10.1002/embr.201337974						
Comment[SecondaryAccession]	GSE54741						
Comment[GEOReleaseDate]	2014-04-03						
Comment[ArrayExpressSubmissionDate]	2014-02-06						
Comment[GEOLastUpdateDate]	2014-04-03						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-54741.sdrf.txt