|
| Status |
Public on Dec 03, 2014 |
| Title |
CTD14-t0_vs_CTD14-t30min+0.7M NaCl Rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
CTD14 treated with 0.7M NaCl for 30 min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CTD14
treatment: 0.7M NaCl for 30 min
|
| Treatment protocol |
Pre-warmed NaCl in YPD added to each culture to a final concentration of 0.7M NaCl
|
| Growth protocol |
S. cerevisiae strains grown in rich YPD mediumin batch-culture with shaking at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol lysis to isolate total RNA
|
| Label |
Oyster 550
|
| Label protocol |
Amino-allyl-dUTP incorporated into generated cDNA; post-synthesis coupling to cyanine dyes
|
| |
|
| Channel 2 |
| Source name |
CTD14 - unstressed t0 min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CTD14
treatment: unstressed t0 min
|
| Treatment protocol |
Pre-warmed NaCl in YPD added to each culture to a final concentration of 0.7M NaCl
|
| Growth protocol |
S. cerevisiae strains grown in rich YPD mediumin batch-culture with shaking at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol lysis to isolate total RNA
|
| Label |
Oyster 650
|
| Label protocol |
Amino-allyl-dUTP incorporated into generated cDNA; post-synthesis coupling to cyanine dyes
|
| |
|
| |
| Hybridization protocol |
Hybridization on Maui hyb station according to Nimblegen and Maui protocols
|
| Scan protocol |
Axon GenePix Scanner
|
| Description |
CTD14 grow in YPD 30C and exposed to 0.7M NaCl for 30 min
|
| Data processing |
Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal, media signal within ORFs was compared for each channel, and log2(red/green) values were median-centered such that the average of all values = 0. Values in the matrix represent log2 fold-change in t30min vs t0min (unstressed) sample for each denoted strain; Data have been converted so that positive log2 values correspond to gene induction (i.e. higher transcript abundance in T30 sample) and negative log2 values represent gene repression (i.e. higher transcript abundance in unstressed T0 sample).
|
| |
|
| Submission date |
Aug 25, 2014 |
| Last update date |
Dec 03, 2014 |
| Contact name |
Audrey Gasch |
| E-mail(s) |
agasch@wisc.edu
|
| Phone |
6082650859
|
| Organization name |
university of wisconsin, madison
|
| Department |
genetics
|
| Street address |
425G Henry mall
|
| City |
madison |
| State/province |
wi |
| ZIP/Postal code |
53713 |
| Country |
USA |
| |
|
| Platform ID |
GPL15778 |
| Series (2) |
| GSE60613 |
Coordination and interconnectivity in the inferred stress-activated signaling network from yeast |
| GSE60700 |
Modification of C-terminal Domain (CTD) of RPB1 plays a role in transcriptome change upon salt stress |
|
