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Title: Nucleosome maps in S. cerevisiae at varying phosphate concentrations      
dateReleased:
08-01-2011
description:
Genome wide maps of nucleosome occupancy in yeast have been produced through deep sequencing of nuclease-protected DNA. These maps have been obtained from crosslinked chromatin in vivo at varying phosphate concentrations (no phoshate and 10mM phosphate concentration). Here, we analyze these maps in combination with existing TF binding data (Harbison et al., Nature, 2004, 431(7004):99-104), and with new gene expression experiments reported here (GSE26770). We also confirm previous conclusions that the intrinsic,sequence dependent binding of nucleosomes helps determine the localization of TF binding sites. High-throughput sequencing of yeast nucleosomal DNA at varying phosphate concentration. Yeast S. cerevisiae (strain: PHO4-MYC::TRP1; CBF1-3HA::LEU2) in log phase was grown in PNB medium with no phosphate for 3 hours and then shifted to various phosphate concentration (0mM and 10 mM) for 80 minutes. After micrococcal nuclease treatment, reverse crosslink and gel purification mononucleosome were isolated. The sequencing by Illumina Solexa following manufacturer protocol has provided mononucleosomal maps in yeast genome (Oct. 2003 SGD/sacSer1 genome release) at two phosphate concentrations (starvation and normal).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-26392
refinement:
raw
alternateIdentifiers:
26392
keywords:
functional genomics
dateModified:
08-21-2013
availability:
available
types:
gene expression
name:
Saccharomyces cerevisiae
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26392/E-GEOD-26392.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26392/E-GEOD-26392.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26392
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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