|
| Status |
Public on Jan 15, 2013 |
| Title |
bmhhdac-2 |
| Sample type |
RNA |
| |
|
| Source name |
Exponentially growing cells, CTY-TY44
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: KBY3
genetic background: W303-1A
genotype/variation: bmh1-170ts bmh2∆ hda1∆ rpd3∆
carbon source: 5% glucose
growth phase: exponential
|
| Treatment protocol |
Growth in YP medium with 5% glucose as the carbon source.
|
| Growth protocol |
Cells were incubated overnight in YP medium containing 5% glucose on a flask shaker at 30˚C until they reached an optical density at 600 nm of between 0.7 and 1.3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by the standard hot acid phenol method for yeast.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNAs were prepared from 250 ng of each total RNA and fragmented using the Affymetrix 3' IVT Express Kit.
|
| |
|
| Hybridization protocol |
Fragmented cRNAs were loaded into Yeast 2.0 arrays and rotated at 60 rpm for 16 h in an Affymetrix hybridization oven set at 45˚C. Hybridized arrays were then stained and washed using an Affymetrix Fluidics Station 450 as described in the Fluidics Station manual for Yeast 2.0 arrays.
|
| Scan protocol |
The stained arrays were scanned using an Affymetrix GeneChip scanner.
|
| Description |
bmhhdac-11
|
| Data processing |
The data were analyzed using various Bioconductor packages for the R statistical analysis programming environment. First, all S. pombe probe sets, individual S. cerevisiae probes whose sequence contains a SNP in the W303 genome sequence as determined by the Saccharomyces Genome Resequencing Project (Sanger Institute in Cambridge, U.K.), and probes from probe sets that overlapped deletions present in the W303 genome as determined by Schacherer et al. (Nature. 2009. 458:342-5) were filtered from the cdf environment created from the information in the yeast2cdf package. This was accomplished using the Bioconductor altcdfenvs and makecdfenv packages. Then, the probe intensities were summarized using the Bioconductor affy package. Background was corrected using RMA, and then the data was normalized by Quantiles and summarized by Median polish.
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
Jan 15, 2013 |
| Contact name |
Kenneth M Dombek |
| E-mail(s) |
[email protected]
|
| Phone |
206-616-9259
|
| Organization name |
University of Washington
|
| Department |
Biochemistry
|
| Lab |
E.T. Young
|
| Street address |
1959 Pacific St. N.E.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-7350 |
| Country |
USA |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE40116 |
mRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants |
|
