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Sample GSM414911 Query DataSets for GSM414911
Status Public on Mar 01, 2010
Title Sp Gcn5-myc enrichment normal conditions
Sample type genomic
 
Channel 1
Source name strain Hu2020 (ChIP fraction)
Organism Saccharomyces cerevisiae/Schizosaccharomyces pombe fusant
Characteristics agent: no treatment
time: n/a
tag: myc
genotype: h-, gcn5-myc::KanMX6, leu1-32, ura4-D18, ade6-M210
antibody: monoclonal anti-c-Myc
Treatment protocol untreated
Growth protocol Yeast cells grow at 25°C in YPD medium to log phase.
Extracted molecule genomic DNA
Extraction protocol Experimental procedure was essentially according to Johnsson ect, EMBO reports, 2009 (in press)
Label biotin
Label protocol Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol: affymetrix chromatin immunoprecipitation assay protocol. 2005-2006
 
Channel 2
Source name strain Fy368 (wild type control)
Organism Saccharomyces cerevisiae/Schizosaccharomyces pombe fusant
Characteristics agent: no treatment
genotype: h-, leu1-32, ura4-D18, ade6-M210
Treatment protocol untreated
Growth protocol Yeast cells grow at 25°C in YPD medium to log phase.
Extracted molecule genomic DNA
Extraction protocol Experimental procedure was essentially according to Johnsson ect, EMBO reports, 2009 (in press)
Label biotin
Label protocol Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol: affymetrix chromatin immunoprecipitation assay protocol. 2005-2006
 
 
Hybridization protocol Fragmented genomic DNA was hybridized to Affymetrix GeneChip S. cerevisiae Tilling 1.0R according to Affymetrix chromatin immunoprecipitation assay protocol. 2005-2006
Scan protocol According to affymetrix chromatin immunoprecipitation assay protocol. 2005-2006
Description This file contains genome-wide signal intensity for Gcn5-myc enrichment under normal conditions in S. pombe. Two experimental samples and two control samples are used for analysis. MAT (see data processing) was used for data processing with the band width setting at 250, max gap at 300 and min probe at 10.
Data processing Model-based analysis of tilling-array (MAT) was used. Johnson WE etc. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462.
MAT data processing with the band width setting at 250, max gap at 300 and min probe at 10.
 
Submission date Jun 09, 2009
Last update date Jan 08, 2010
Contact name Anthony Wright
E-mail(s) yongtao.xue.franzen@ki.se
Organization name Karolinska Institute
Lab Anthony Wright
Street address Blickagången 6
City Huddinge
ZIP/Postal code 141 57
Country Sweden
 
Platform ID GPL7715
Series (2)
GSE16514 Genome-wide localization of Gcn5 under normal and stress conditions in S. cerevisiae and S. pombe
GSE16556 Role of Gcn5 in KCl stress adaptation in S. cerevisiae and S. pombe: transcriptional and genomic analyses

Supplementary file Size Download File type/resource
GSM414911_Sp_Gcn5-myc_enrichment.bar.gz 6.0 Mb (ftp)(http) BAR
GSM414911_sp_Gcn5_replicate_1.CEL.gz 11.8 Mb (ftp)(http) CEL
GSM414911_sp_Gcn5_replicate_2.CEL.gz 11.5 Mb (ftp)(http) CEL
GSM414911_sp_control_replicate_1.CEL.gz 11.0 Mb (ftp)(http) CEL
GSM414911_sp_control_replicate_2.CEL.gz 11.9 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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