|
| Status |
Public on Feb 08, 2012 |
| Title |
6-NDA-treated, biological repA1 |
| Sample type |
RNA |
| |
|
| Source name |
Yeast cells treated with 6-NDA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: S288C
|
| Treatment protocol |
Cultures of S. cerevisiae strain S288C were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with either DMSO (0.25%) or 6-NDA at the IC50 concentration (2.2 ug/ml). When OD600 of 0.5 was reached, cells were harvested and frozen. Two biological replicate cultures were grown for each treatment, and RNA from each replicate was hybridized to 2 independent arrays, resulting in 4 hybridizations for each treatment.
|
| Growth protocol |
All cultures were grown in SD broth (2% dextrose, 0.67% yeast nitrogen base without amino acids, MOPS buffered, pH 7.0) at 30 degrees, with shaking at 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Midi kit was used for total RNA extraction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol were used. GeneChip Yeast Genome 2.0 arrays were used.
|
| Scan protocol |
Affymetrix GenChip Scanner 3000 default parameters were used.
|
| Description |
Gene expression data from 6-NDA-treated yeast cells (repA, hyb1)
|
| Data processing |
Image analysis, scaling (TGT = 1000), and probeset-level data analysis was performed using default parameters in GCOS v1.1
|
| |
|
| Submission date |
Feb 07, 2012 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Ameeta Agarwal |
| E-mail(s) |
aagarwal@olemiss.edu
|
| Phone |
662-915-1218
|
| Organization name |
University of Mississippi
|
| Department |
National Center for Natural Products Research
|
| Street address |
NCNPR, Room 2049
|
| City |
University |
| State/province |
MS |
| ZIP/Postal code |
38677 |
| Country |
USA |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE35604 |
Gene expression response to the antifungal compound 6-Nonadecynoic acid (6-NDA) in Saccharomyces cerevisiae and Candida albicans |
|
