|
| Status |
Public on Feb 21, 2009 |
| Title |
Candida albicans cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R3). |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Candida albicans, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #3
|
| Organism |
Candida albicans |
| Characteristics |
strain: wild type cells (SC5314)
|
| Treatment protocol |
Cell cultures were treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 60 minutes at 30°C.
|
| Growth protocol |
Cell cultures were grown in YPD liquid medium at 30°C to an O.D600=0.5, and treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 60 minutes at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a RiboPureTM-Yeast RNA extraction kit (Ambion Inc).
|
| Label |
Cy5
|
| Label protocol |
cDNA from 15 ug of total RNA was synthesized using an AffinityScriptTM-Multiple Temperature Reverse Transcriptase kit (Stratagene). cDNA generated from drug vehicle treated cells were used as reference and labeled with Cy3 (Amersham) and cDNA synthesized from rapamycin treated cells were labeled with Cy5 (Amersham) and used as the experimental sample.
|
| |
|
| Channel 2 |
| Source name |
Candida albicans drug vehicle (90% EtOH 10% Tween-20)
|
| Organism |
Candida albicans |
| Characteristics |
strain: wild type cells (SC5314)
|
| Growth protocol |
Cell cultures were grown in YPD liquid medium at 30°C to an O.D600=0.5, and treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 60 minutes at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a RiboPureTM-Yeast RNA extraction kit (Ambion Inc).
|
| Label |
Cy3
|
| Label protocol |
cDNA from 15 ug of total RNA was synthesized using an AffinityScriptTM-Multiple Temperature Reverse Transcriptase kit (Stratagene). cDNA generated from drug vehicle treated cells were used as reference and labeled with Cy3 (Amersham) and cDNA synthesized from rapamycin treated cells were labeled with Cy5 (Amersham) and used as the experimental sample.
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA were hybridized overnight at 42°C to a 70-mer C. albicans AROS V1.2 oligo microarray set (OPERON technologies) printed at Duke University microarray facility.
|
| Scan protocol |
Hybridized arrays were scanned with an Axon GenePix scanner (GenePix 400B, Molecular Devices).
|
| Description |
Data was extracted using GenePix Pro 4 software (Molecular Devices).
|
| Data processing |
Value corresponds to Normalized log2 Cy5(635 nm)/Cy3(532 nm) ratio of medians extracted by GenePix Pro 4 software and normalized by Lowess (per spot/per chip) using GeneSpring software.
|
| |
|
| Submission date |
Oct 13, 2008 |
| Last update date |
Feb 20, 2009 |
| Contact name |
Robert J Bastidas |
| E-mail(s) |
[email protected]
|
| Phone |
919-684-2809
|
| Organization name |
Duke University
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Cardenas/Heitman Lab
|
| Street address |
322 CARL, Research Drive Box 3546
|
| City |
Durham |
| State/province |
N.C |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL7476 |
| Series (1) |
| GSE13176 |
The protein kinase Tor1 regulates adhesin expression in Candida albicans |
|
