Comment[ArrayExpressAccession]	E-GEOD-6667
Investigation Title	PolII occupancy
Comment[Submitted Name]	PolII occupancy
Publication Title	Dynamics of replication-independent histone turnover in budding yeast.
Publication Author List	Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ
Publication DOI	
PubMed ID	17347438
Experimental Design	ChIP-chip by tiling array
Experimental Design Term Source REF	EFO
Public Release Date	2007-05-16
Experiment Description	Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states. Keywords: Chip-chip, PolII ChIP-chip for RNA polymerase II (vs genomic DNA).										
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Term Source Name	EFO
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Person Last Name	Kaplan	Dion	Kaplan	Kim	Buratowski	Friedman	Rando				
Person First Name	Tommy	Michael	Tommy	Minkyu	Stephen	Nir	Oliver				
Person Mid Initials		F					J				
Person Email	tommy@cs.huji.ac.il										
Person Affiliation	Hebrew University										
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Person Address	School of Computer Science, Hebrew University, Ross bldg, Jerusalem, Israel										
Person Roles	submitter										
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Protocol Name	P-GSE6667-2	P-GSE6667-1	P-GSE6667-3	P-GSE6667-4	P-GSE6667-9	P-GSE6667-8	P-GSE6667-11	P-GSE6667-5	P-GSE6667-6	P-GSE6667-7	P-GSE6667-10
Protocol Description	ID_REF = <br>VALUE = log2(Pol II IP/Genomic) t0 rep2<br>t0-PolII-rep2-Int = PolII IP t0 rep2<br>t0-Genomic-rep2-Int = Genomic t0 rep1	ID_REF = <br>VALUE = log2(Pol II IP/Genomic) t0 rep1<br>t0-PolII-rep1-Int = PolII IP t0 rep1<br>t0-Genomic-rep1-Int = Genomic t0 rep1	ID_REF = <br>VALUE = log2(Pol II IP/Genomic) t60 rep1<br>t60-PolII-rep1-Int = PolII IP t60 rep1<br>t60-Genomic-rep1-Int = Genomic t60 rep1	ID_REF = <br>VALUE = log2(Pol II IP/Genomic) t60 rep2<br>t60-PolII-rep2-Int = PolII IP t60 rep2<br>t60-Genomic-rep2-Int = Genomic t60 rep2	was scanned according to Agilent protocol	was hybridized according to Agilent protocol	t=60 (3 hours of alpha factor, 60 minutes after galactose shift)	t=0 (3 hours of alpha factor, no galactose)	See [Kim et al, Nature 432(7016):517-22 (2004)]	See [Kim et al, Nature 432(7016):517-22 (2004)]	log2(Cy5/Cy3)
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Protocol Type	bioassay_data_transformation	bioassay_data_transformation	bioassay_data_transformation	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction
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Comment[SecondaryAccession]	GSE6667										
Comment[GEOLastUpdateDate]	2009-03-15
Comment[GEOReleaseDate]	2007-05-15
Comment[ArrayExpressSubmissionDate]	2007-01-06
SDRF File	E-GEOD-6667.sdrf.txt