|
| Status |
Public on Sep 20, 2009 |
| Title |
wt_2 |
| Sample type |
RNA |
| |
|
| Source name |
wild type, rep 2
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: wild type
replicate: 2
experiment date: 1-30-07
|
| Growth protocol |
Cells were grown at 30 °C in asynchronous cultures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested for Total RNA extraction with hot phenol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix (One-Cycle) protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
wt_2
|
| Data processing |
The .CEL files are read into R and processed with RMA (Irizarry et al., 2003) to generate log2 scores of the probe set intensities. The array intensities are then linearly modeled to find coefficients of expression between the various mutants and wt using Limma (Smyth, 2004).
|
| |
|
| Submission date |
Jul 22, 2009 |
| Last update date |
Jul 27, 2009 |
| Contact name |
Susan Forsburg |
| E-mail(s) |
[email protected]
|
| Phone |
213-740-7342
|
| Fax |
213-740-8631
|
| URL |
http://www.pombe.net
|
| Organization name |
University of Southern California
|
| Department |
Molecular and Computational Biology
|
| Lab |
Forsburg
|
| Street address |
1050 Childs Way, RRI 201B
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089-2910 |
| Country |
USA |
| |
|
| Platform ID |
GPL2529 |
| Series (2) |
| GSE17262 |
S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation, Affymetrix dataset |
| GSE17298 |
Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation |
|
