|
| Status |
Public on Jul 18, 2015 |
| Title |
WTvsM_Pre_oxidation_rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT Pre-oxidation
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: LDY1033
genotype: wildtype
|
| Treatment protocol |
Fresh H2O2 was added to the remaining culture (from growth protocol) to a 1.0 mM final concentration and each culture incubated for 10 min at 30 °C, after which 200 ml of culture was removed, spun, and frozen as above to generate the 10minOxidation samples. This was repeated with another 200 ml of cells 1 hr after H2O2 addition to generate the 60minOxidation samples. The remaining culture was then pelleted, YPD+H2O2 media removed, cells resuspended in 250 ml YPD, and culture incubated for 1 hr at 30 °C. Cells were then pelleted and frozen as before to generate the 120minOxidation samples, which actually are 60 min oxidative stress followed by 60 min no oxidative stress.
|
| Growth protocol |
Wild-type and kap108∆ cells were grown to A600 = 0.3 in 1L YPD. Two hundred ml of culture was removed, spun at 3,000rpm for 10 min, and frozen at -80 °C. This sample was used as the pre-oxidation condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from cell pellets was isolated using the RiboPure-Yeast RNA isolation kit (Ambion, Inc.)
|
| Label |
Cy3
|
| Label protocol |
RNA generated from wild-type cell extracts was labeled with Cy3 and from ∆Kap108 cells was labeled with Cy5 by MoGene, LC
|
| |
|
| Channel 2 |
| Source name |
∆Kap108 Pre-oxidation
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: KBY 1357
genotype: deltaKap108
|
| Treatment protocol |
Fresh H2O2 was added to the remaining culture (from growth protocol) to a 1.0 mM final concentration and each culture incubated for 10 min at 30 °C, after which 200 ml of culture was removed, spun, and frozen as above to generate the 10minOxidation samples. This was repeated with another 200 ml of cells 1 hr after H2O2 addition to generate the 60minOxidation samples. The remaining culture was then pelleted, YPD+H2O2 media removed, cells resuspended in 250 ml YPD, and culture incubated for 1 hr at 30 °C. Cells were then pelleted and frozen as before to generate the 120minOxidation samples, which actually are 60 min oxidative stress followed by 60 min no oxidative stress.
|
| Growth protocol |
Wild-type and kap108∆ cells were grown to A600 = 0.3 in 1L YPD. Two hundred ml of culture was removed, spun at 3,000rpm for 10 min, and frozen at -80 °C. This sample was used as the pre-oxidation condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from cell pellets was isolated using the RiboPure-Yeast RNA isolation kit (Ambion, Inc.)
|
| Label |
Cy5
|
| Label protocol |
RNA generated from wild-type cell extracts was labeled with Cy3 and from ∆Kap108 cells was labeled with Cy5 by MoGene, LC
|
| |
|
| |
| Hybridization protocol |
RNA probes were hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC
|
| Scan protocol |
Scanned my MoGene, LC on Agilent Technologies Scanner G2505B US22502547. Protocols are GE2-v5_95_Feb07 for replicate 1/3 and GE2-v5_10_Apr08 for replicates 2/3 and 3/3
|
| Description |
Biological Replicate 3 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .
|
| Data processing |
Scanner performed background correction and linear lowess normalization. Further normalization took place by using GeneSpring GX 13.0 to perform a log2 transformation and percentile shift to the 75th percentile
|
| |
|
| Submission date |
Jul 17, 2015 |
| Last update date |
Jul 18, 2015 |
| Contact name |
Ken Belanger |
| E-mail(s) |
kbelanger@colgate.edu
|
| Phone |
315-228-7870
|
| Organization name |
Colgate University
|
| Department |
Biology
|
| Street address |
13 Oak Drive
|
| City |
Hamilton |
| State/province |
NY |
| ZIP/Postal code |
13346 |
| Country |
USA |
| |
|
| Platform ID |
GPL9294 |
| Series (1) |
| GSE71068 |
Yeast Whole Genome Analysis - Wild-Type vs kap108∆ cells |
|
