|
| Status |
Public on Feb 28, 2013 |
| Title |
Gene expression analysis following methionine addition to wild type cells |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT minus methionine
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: BY4742 (MATα his3∆1 leu2∆0 ura3∆0 lys2∆0)
|
| Growth protocol |
Wild type, nup157∆, nup170∆, and nup188∆ cells were cultured at 30˚C in YPD medium to an OD600 of 0.8 and harvested. PMET3-HA3-STH1 cells were grown at 30˚C in synthetic complete (SC) medium lacking methionine to mid-logarithmic phase (0 h) and STH1 was repressed by the addition of methionine to a final concentration of 200 µg/mL for 8 hrs. Following 8 hrs of repression, methionine was removed by extensive washes with SC medium lacking methionine and STH1 was reinduced by growth in SC medium lacking methionine for an additional 4 hrs. Cells were harvested at 0 hr, 2 hr and following 4 hrs of reinduction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot acidic phenol extraction.
|
| Label |
Cy5
|
| Label protocol |
Agilent yeast gene expression array protocol
|
| |
|
| Channel 2 |
| Source name |
WT plus methionine
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742 (MATα his3∆1 leu2∆0 ura3∆0 lys2∆0)
|
| Growth protocol |
Wild type, nup157∆, nup170∆, and nup188∆ cells were cultured at 30˚C in YPD medium to an OD600 of 0.8 and harvested. PMET3-HA3-STH1 cells were grown at 30˚C in synthetic complete (SC) medium lacking methionine to mid-logarithmic phase (0 h) and STH1 was repressed by the addition of methionine to a final concentration of 200 µg/mL for 8 hrs. Following 8 hrs of repression, methionine was removed by extensive washes with SC medium lacking methionine and STH1 was reinduced by growth in SC medium lacking methionine for an additional 4 hrs. Cells were harvested at 0 hr, 2 hr and following 4 hrs of reinduction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using hot acidic phenol extraction.
|
| Label |
Cy3
|
| Label protocol |
Agilent yeast gene expression array protocol
|
| |
|
| |
| Hybridization protocol |
Agilent yeast gene expression array protocol
|
| Scan protocol |
Agilent yeast gene expression array protocol
|
| Description |
Two color microarrays, comparing RNA from the experimental condition (WT cells grown in medium containing 200 µg/mL methionine) to RNA from the control (WT cells grown in medium lacking methionine), were performed using Agilent whole-genome S. cerevisiae arrays.
|
| Data processing |
Differentially expressed genes were identified by maximum-likelihood analysis (Ideker et al., 2000 and Smith et al., 2002) with lambda ≥ 100, with the exception of sth1-deplete 2hr and sth1-reinduction 4hr (lambda ≥ 50). Significantly affected genes in each condition were identified by a ≥ 2-fold change in gene expression when compared to the corresponding control strain.
Please refer to the following links for the .clone file-format:
http://db.systemsbiology.net/software/VERAandSAM/doc/VERAandSAM_win.html
http://db.systemsbiology.net/software/VERAandSAM/doc/fileFormat.html
|
| |
|
| Submission date |
Mar 26, 2012 |
| Last update date |
Feb 28, 2013 |
| Contact name |
Yakun Wan |
| E-mail(s) |
ywansystemsbiology@gmail.com
|
| Organization name |
Southeast University
|
| Street address |
Sipailou #2
|
| City |
Nanjing |
| ZIP/Postal code |
210096 |
| Country |
China |
| |
|
| Platform ID |
GPL6068 |
| Series (2) |
| GSE36793 |
A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent microarrays] |
| GSE36795 |
A role for the nucleoporin Nup170p in chromatin structure and gene silencing |
|
