|
| Status |
Public on May 01, 2005 |
| Title |
S.cerevisiae S288C, about one doubling time after treatment with fenhexamid |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source Name |
S. cerevisiae treated with I50 concentration of fenhexamid
|
| Organism(s) |
Saccharomyces cerevisiae |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source Name |
S. cerevisiae treated with solvent (DMSO)
|
| Organism(s) |
Saccharomyces cerevisiae |
| Extracted molecule |
total RNA |
| |
|
| |
| Description |
Cultures were grown in synthetic dextrose medium, pH 7.0. Cultures were started from an overnight culture diluted to A600=0.10. Fenhexamid, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves. Controls received an equivalent amount of DMSO. Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA. The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4). Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics). The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenhexamid-Cy3=control, ch2=Fenhexamid-Cy5=treatment with fenhexamid
Ontario Cancer Inst. Bar Code no. 12257497
|
| |
|
| Submission date |
Mar 17, 2005 |
| Contact name |
Isabelle Ann Kagan |
| E-mail(s) |
ikagan@msa-stoneville.ars.usda.gov
|
| Phone |
1-859-257-4610
|
| Fax |
1-859-257-3334
|
| Organization name |
National Center for Natural Products Research
|
| Department |
US Department of Agriculture
|
| Lab |
ARS, Natural Products Utilization Research Unit
|
| Street address |
University Ave.
|
| City |
University |
| State/province |
MS |
| ZIP/Postal code |
38677 |
| Country |
USA |
| |
|
| Platform ID |
GPL1877 |
| Series (1) |
| GSE2412 |
Agricultural sterol biosynthesis inhibitor fungicides |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log2 ratio of ch2/ch1 (treatment divided by control) |
| ch2/ch1 |
ratio of treatment intensity to control intensity |
| ch1 Intensity |
mean fluorescence intensity (Cy3) of control cDNA |
| ch2 Intensity |
mean fluorescence intensity (Cy5) of cDNA from fenhexamid treatment |
| ch1 Background |
mean ch1 background fluorescence intensity |
| ch1 Intensity Std Dev |
standard deviation of mean control fluorescence intensity |
| ch1 Background Std Dev |
standard deviation of mean control background fluorescence intensity |
| ch1 Diameter |
diameter for control spot |
| ch1 Area |
area of spot for control |
| ch1 Circularity |
degree to which control spot geometry approximates a circle |
| ch1 Spot Uniformity |
uniformity of pixels used to calculate control spot intensity |
| ch1 Bkg. Uniformity |
|
| ch1 Signal Noise Ratio |
ratio of control spot intensity to std dev of background of all spots on microarray |
| ch2 Background |
mean background fluorescence intensity of treatment |
| ch2 Intensity Std Dev |
standard deviation of mean fluorescence intensity of treatment |
| ch2 Background Std Dev |
standard deviation of mean ch2 background fluorescence intensity |
| ch2 Diameter |
diameter for ch2 spot |
| ch2 Area |
area of spot for ch2 |
| ch2 Circularity |
degree to which treatment spot geometry approximates a circle |
| ch2 Spot Uniformity |
uniformity of pixels used to calculate spot intensity for treatment |
| ch2 Bkg. Uniformity |
uniformity of pixels used to calculate background of treatment spot |
| ch2 Signal Noise Ratio |
ratio of treatment spot intensity to std dev of background of all spots on microarray |
