|
| Status |
Public on Sep 04, 2010 |
| Title |
WT vs rim101 mutant gene expression |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT in capsule inducing medium
|
| Organism |
Cryptococcus neoformans var. grubii |
| Characteristics |
strain: H99
growth medium: DMEM
|
| Biomaterial provider |
Alspaugh Laboratory, Duke University Medical Center
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA) following manufacturer's instructions.
|
| Label |
Cy3,Cy5
|
| Label protocol |
Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).
|
| |
|
| Channel 2 |
| Source name |
rim101 in capsule inducing medium
|
| Organism |
Cryptococcus neoformans var. grubii |
| Characteristics |
growth medium: DMEM
strain: rim101
|
| Biomaterial provider |
Alspaugh Laboratory, Duke University Medical Center
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA) following manufacturer's instructions.
|
| Label |
Cy3,Cy5
|
| Label protocol |
Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://www.genome.duke.edu/cores/microarray/).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://www.genome.duke.edu/cores/microarray/).
|
| Scan protocol |
Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://www.genome.duke.edu/cores/microarray/).
|
| Description |
dye swaps were performed
|
| Data processing |
Data was analyzed using JMP genomics (SAS institute, Cary NC) and initial background subtraction was performed. We used ANOVA normalization and FDR analysis to calculate differences between treatment effects for pairs of inducing conditions. Genes were considered for further evaluation if they showed log2-transformed fold changes with a p-value < 0.02.
|
| |
|
| Submission date |
Sep 01, 2010 |
| Last update date |
Sep 03, 2010 |
| Contact name |
Michael S Price |
| E-mail(s) |
msprice2@liberty.edu
|
| Phone |
434-592-7277
|
| Organization name |
Liberty University
|
| Department |
Biology & Chemistry
|
| Street address |
1971 University Blvd.
|
| City |
Lynchburg |
| State/province |
VA |
| ZIP/Postal code |
24515 |
| Country |
USA |
| |
|
| Platform ID |
GPL4009 |
| Series (1) |
| GSE23929 |
WT vs rim101 mutant gene expression under capsule inducing conditions |
|
