|
| Status |
Public on Dec 12, 2012 |
| Title |
Forward Trans Expt 1 - MBY38 + no Dox 7 hrs |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Forward Transition Expt - Cy3 Reference Sample
|
| Organism |
Candida albicans |
| Characteristics |
strain: MBY38
genotype/variation: TetO-UME6
other: Forward Transition Pooled Reference: Equal aliquots of the 21 sample RNAs (Dox dosage of 1.0 ug/ml (n=11) or 0 ug/ml (n=10) at time points from 0 to 10 hours) were combined to create a pooled reference sample.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot Acid Phenol Extraction Protocol
Other: RNA was isolated from C. albicans cells using the hot acid phenol method. Total RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.
|
| Label |
cy3
|
| Label protocol |
Cy3 Labeling Protocol
Other: Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 uL), 3DNA capture reagent with Cy5 (2.5 uL), SDS-based hybridization buffer (vial 6-Genisphere) (26 uL), and RNase/DNnase-free water (21 uL). The secondary hybridization solution was incubated in the dark at 80 C for 10 min., then at 50 C for 15 min.
|
| |
|
| Channel 2 |
| Source name |
Forward Transition Expt - MBY38 + no Dox 7 hrs - Cy5
|
| Organism |
Candida albicans |
| Characteristics |
strain: MBY38
genotype/variation: TetO-UME6
|
| Treatment protocol |
Treatment time: 7 hours
Treatment temperature: 30 C
In-vitro treatment: For the experiment in which C. albicans undergoes the yeast-pseudohyphal-hyphal transition in response to increased UME6 levels over a time course, the tetO-UME6 (MBY38) strain was grown overnight at 30°C in YEPD medium + 1.0 µg/mL Dox to OD600 ~ 0.5. 50 mL aliquots of cells were then washed 1X in prewarmed YEPD medium at 30°C and used to inoculate 1.5 L of YEPD medium in the presence or absence of 1.0 µg/mL Dox . Cultures were grown at 30°C and cells were harvested for RNA extraction at each hour for 10 hours. Cells for the 0 hour time point were collected from the tetO-UME6 overnight culture just prior to washing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot Acid Phenol Extraction Protocol
Other: RNA was isolated from C. albicans cells using the hot acid phenol method. Total RNA quality was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer's recommendations.
|
| Label |
cy5
|
| Label protocol |
Cy5 Labeling Protocol
Other: Secondary hybridization was carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere). For each reaction, the following were added: 3DNA capture reagent with Cy3 (2.5 uL), 3DNA capture reagent with Cy5 (2.5 uL), SDS-based hybridization buffer (vial 6-Genisphere) (26 uL), and RNase/DNnase-free water (21 uL). The secondary hybridization solution was incubated in the dark at 80 C for 10 min., then at 50 C for 15 min.
|
| |
|
| |
| Hybridization protocol |
Sample Hybridization Protocol
Other: Hybridization was performed by adding 48 uL of secondary hybridization solution to the slide under a supported glass coverslip and carried out at 65 C for 3 hr. at high humidity in the dark. At hybridization termination, arrays were gently submerged into 2X SSC, 0.2% SDS (at 65 C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. To prevent fluorophore degradation, the arrays were treated with Dyesaver (Genisphere).
|
| Scan protocol |
ScanArray Scanning Protocol
Other: Arrays were scanned using a ScanArray Express HT (Serial No.: 680078) microarray scanner along with ScanArray Express 2.00 image analysis software.
|
| Description |
No additional information.
|
| Data processing |
Forward Transition Expt Data Processing
Calculation Method: Microarray data was normalized using the Lowess method (Y.H. Yang, 2001) and filtered using Partek software to only include spots showing a median signal intensity >200 and signal-to-noise ratio >2. The forward yeast-pseudohyphal-hyphal transition time course experiment was repeated twice (two independent biological replicates). For each biological replicate experiment, the median signal ratio (ratio of the median signal intensity of each spot) for the zero time point versus reference was first determined based on 3 technical replicates (one of which was performed using reverse fluors) using cDNA from the same total RNA preparation. Next, the signal ratio for each time point sample versus reference was divided by the median signal ratio for the zero time point versus reference.
|
| |
|
| Submission date |
Jul 26, 2012 |
| Last update date |
Dec 12, 2012 |
| Contact name |
David Kadosh |
| E-mail(s) |
kadosh@uthscsa.edu
|
| Organization name |
University of Texas Health Science Center at San Antonio
|
| Department |
Microbiology and Immunology
|
| Lab |
Kadosh Lab 5.023V
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL15843 |
| Series (1) |
| GSE39677 |
A Genome-wide Transcriptional Analysis of Morphology Determination in Candida albicans |
|
