|
| Status |
Public on Apr 23, 2009 |
| Title |
SC_HaploidDeletionPool_AcuteH2O2_rep4 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
0.4 mM H2O2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
A pool of the 4,831 viable haploid deletion strains was created from individual collections kept in glycerol stock and divided into 1 mL aliquots stored at -80° C. A single aliquot of pooled deletion strains was diluted in 15 mL YPD media and grown in a rotating wheel at 30° C to OD600 = 0.6. The sample was then split into two 6.5 mL portions. After 45 minutes of continued growth at 30° C, the aliquot corresponding to this channel was treated with a high dose (final concentration in media: 0.4 mM) of hydrogen peroxide. After 1 hour of treatment, the cells were harvested by centrifugation at 3000 rpm for 5 min and resuspended in 50 mL of YPD media. After 5 hours of growth, the cells were once again harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen and stored at 80° C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets using a glass bead preparation.
|
| Label |
Cy5
|
| Label protocol |
DNA labeling followed the protocol of Yuan et al. 2005. Briefly, asymmetric PCR was used to amplify unique tag sequences in the genomic DNA of the deletion strains. In each PCR reaction, 1 μg of gDNA was used for labeling.
|
| |
|
| Channel 2 |
| Source name |
Untreated
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
A pool of the 4,831 viable haploid deletion strains was created from individual collections kept in glycerol stock and divided into 1 mL aliquots stored at -80° C. A single aliquot of pooled deletion strains was diluted in 15 mL YPD media and grown in a rotating wheel at 30° C to OD600 = 0.6. The sample was then split into two 6.5 mL portions. After 45 minutes of continued growth at 30° C, the aliquot corresponding to this channel was treated with a sham dose. After 1 hour of treatment, the cells were harvested by centrifugation at 3000 rpm for 5 min and resuspended in 50 mL of YPD media. After 5 hours of growth, the cells were once again harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen and stored at 80° C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets using a glass bead preparation.
|
| Label |
Cy3
|
| Label protocol |
DNA labeling followed the protocol of Yuan et al. 2005. Briefly, asymmetric PCR was used to amplify unique tag sequences in the genomic DNA of the deletion strains. In each PCR reaction, 1 μg of gDNA was used for labeling.
|
| |
|
| |
| Hybridization protocol |
DNA hybridization followed the protocol of Yuan et al. 2005. Slides were hybridized for 16h at 42 degree Celcius in a rotating oven, and washed.
|
| Scan protocol |
Arrays were scanned using a GenePix 4000A or PerkinElmer Scanarray Lite microarray scanner at 10.0 uM and quantified with the GenePix 6.0 software package.
|
| Description |
Haploid deletion mutant pool treated with 0.4 mM H2O2 and compared to untreated cells
|
| Data processing |
Following background-subtraction of individual spots, loess and two-dimensional spatial normalization are performed (default parameters within the R hoptage package). Value is log ratio of normalized intensities.
|
| |
|
| Submission date |
Sep 09, 2008 |
| Last update date |
Apr 23, 2009 |
| Contact name |
Ryan Kelley |
| Organization name |
UCSD
|
| Department |
Bioinformatics
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0412 |
| Country |
USA |
| |
|
| Platform ID |
GPL1444 |
| Series (1) |
| GSE12733 |
Phenotypic profiling of adaptation to oxidative stress |
|
