|
| Status |
Public on Mar 01, 2010 |
| Title |
Sp Gcn5-myc enrichment KCl stress conditions |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
strain Hu2020 (ChIP fraction)
|
| Organism |
Saccharomyces cerevisiae/Schizosaccharomyces pombe fusant |
| Characteristics |
agent: 1M KCl
time: 1hr
tag: myc
genotype: h-, gcn5-myc::KanMX6, leu1-32, ura4-D18, ade6-M210
antibody: monoclonal anti-c-Myc
|
| Treatment protocol |
KCl treatment: cell grown to mid log phase in YES at 25°C, then treated with KCl (final concentration 1M) 60 min
|
| 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 KCl stress 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 |
|
