|
| Status |
Public on Sep 18, 2011 |
| Title |
BY4741 + H2O2 30 min vs 0 min rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BY4741 grown in log phase for 3 doublings
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
|
| Treatment protocol |
BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.
|
| Growth protocol |
All experiments were done in YPD and cells were grown exponentially in YPD for 3 doublings prior to the beginning of any treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414.
|
| Label |
Oyster 550 cyanine dye
|
| Label protocol |
Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414.
|
| |
|
| Channel 2 |
| Source name |
BY4741 grown in log phase for 3 doublings, then exposed to 0.4mM H2O2 (30min)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
|
| Treatment protocol |
BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.
|
| Growth protocol |
All experiments were done in YPD and cells were grown exponentially in YPD for 3 doublings prior to the beginning of any treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414.
|
| Label |
Oyster cyanine 650 dye
|
| Label protocol |
Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414.
|
| |
|
| |
| Hybridization protocol |
As indicated in Gasch AP Methods in Enzymology 350: 393-414.
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner.
|
| Description |
YG9-28A
|
| Data processing |
Data were extracted using GenePix 6.0. Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics. The data was further filtered to retain the information of the genes that had data for at least 60 percent of the 32 arrays done. Analyis of the data was done on the remaining 5615 genes. All values in Matrix file have been adjusted such that a positive log2 value = induced by by treatment (NaCl or H2O2), and a negative log2 value = repressed by treatment (or expressed lower in NaCl or H2O2 treatment).
|
| |
|
| Submission date |
Sep 17, 2011 |
| Last update date |
Sep 18, 2011 |
| Contact name |
Suraiya Ruma Haroon |
| E-mail(s) |
haroon@wisc.edu
|
| Phone |
(608) 265-0863
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Genetics
|
| Lab |
Gasch
|
| Street address |
425 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL5915 |
| Series (1) |
| GSE32196 |
nup42-delta cells pretreated with NaCl lose the altered gene expression in response to H2O2 |
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