|
| Status |
Public on Jul 07, 2012 |
| Title |
nup42-delta 0.4mM H2O2 t20 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
nup42-delta grown in log phase for at least 7 generations, treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: nup42-delta in BY4741 strain
|
| Treatment protocol |
treated with 1 hour of 0.7M NaCl, returned to stress-free media for 4 hours
|
| Growth protocol |
grown in log phase for at least 7 generations
|
| 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 |
nup42-delta grown in log phase for at least 7 generations, then exposed to 0.4mM H2O2 for 20min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: nup42-delta in BY4741 strain
|
| Treatment protocol |
exposed to 0.4mM H2O2 for 20min
|
| Growth protocol |
grown in log phase for at least 7 generations
|
| 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 |
cDNA labeled with Oyster cyanine 650 dye and cDNA from second sample labelled with Oyster cyanine 650 dye were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.
|
| Scan protocol |
Arrays were scanned on a GenePix 4000B scanner
|
| Description |
Sample name: nup42-delta naïve t20 vs nup42-delta memory t0
Compare the gene expression of cells exposed to 20 min of 0.4 mM H2O2 compared to basal gene expression in nup42-delta
|
| Data processing |
Data were extracted using NimblegenScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots. The remaining data was quantile normalized using Bioconductor.
normalized, log2 expression ratios (Oyster cyanine 650 dye/Oyster 550 cyanine dye). All values 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 |
Jul 07, 2012 |
| Last update date |
Jul 07, 2012 |
| 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 |
GPL15778 |
| Series (1) |
| GSE32196 |
nup42-delta cells pretreated with NaCl lose the altered gene expression in response to H2O2 |
|
