|
| Status |
Public on Sep 04, 2009 |
| Title |
nrg1 mutant vs. WT under carbon starvation |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Wild-type in carbon starvation
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
strain: H99
genome/variation: wild type
|
| Growth protocol |
C. neoformans H99 was incubated in Synthetic Complete (SC) medium with 2% glucose overnight at 30C, pelleted, and resuspended in SC with 0.1% glucose for 30 minutes at 30C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lyophilized cells using Trizol Reagent (Invitrogen Life Technologies, Carlsbad, CA) following manufacturer's instructions.
|
| Label |
For 0319_3022_CU_383_CNWash_WT-NRG1_PooledRef.gpr and 0319_3021_CU_382_CNWash_WT-NRG1_PooledRef_scan2.gpr TEST=Cy5 and reference=Cy3. Dyes were swapped for 0362_4077_CU_342_CNWash_2-ref_1-H99.gpr.
|
| Label protocol |
Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://microarray.genome.duke.edu/).
|
| |
|
| Channel 2 |
| Source name |
nrg1 mutant in carbon starvation
|
| Organism |
Cryptococcus neoformans var. grubii H99 |
| Characteristics |
strain: H99
genome/variation: nrg1∆ mutant
|
| Growth protocol |
C. neoformans H99 nrg1 mutant was incubated in Synthetic Complete (SC) medium with 2% glucose overnight at 30C, pelleted, and resuspended in SC with 0.1% glucose for 30 minutes at 30C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lyophilized cells using Trizol Reagent (Invitrogen Life Technologies, Carlsbad, CA) following manufacturer's instructions.
|
| Label |
For 0319_3024_CU_242_CNWash_mut-nrg1_PooledRef.gpr and 0319_3023_CU_385_CNWash_mut-nrg1_PooledRef.gpr TEST=Cy5 and reference=Cy3. Dyes were swapped for 0362_4078_CU_343_CNWash_4-ref_3-nrg.gpr.
|
| Label protocol |
Labeling was performed at the Duke University Microarray Facility following the Direct Labeling protocol for spotted arrays (http://microarray.genome.duke.edu/).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed at the Duke University Microarray Facility following the Hybridization protocol (http://microarray.genome.duke.edu/).
|
| Scan protocol |
Slides were scanned at the Duke University Microarray Facility using an Axon Genepix 4000B scanner (http://microarray.genome.duke.edu/).
|
| Description |
Gene expression was compared between WT and nrg1∆ mutant strains of C. neoformans grown in Synthetic Complete medium with 0.1% glucose.
Ch1 Raw data files:
0319_3022_CU_383_CNWash_WT-NRG1_PooledRef.gpr
0319_3021_CU_382_CNWash_WT-NRG1_PooledRef_scan2.gpr
0362_4077_CU_342_CNWash_2-ref_1-H99.gpr
Ch2 Raw data files:
0319_3024_CU_242_CNWash_mut-nrg1_PooledRef.gpr
0319_3023_CU_385_CNWash_mut-nrg1_PooledRef.gpr
0362_4078_CU_343_CNWash_4-ref_3-nrg.gpr
|
| Data processing |
Extracted data were imported into a statistical software package (SAS v8, SAS Institute, Cary, NC), and initial background subtraction was performed. Mixed model analysis of microarray data (Wolfinger, et al., 2001) was used to evaluate differential expression data using approaches presented elsewhere (Chhabra, et al., 2003; Pysz, et al., 2004; Price et al., 2005). We calculated the statistical significance of each genomic element using least squared means estimates of gene-specific treatment effects across pairs of treatments obtained for each gene under each treatment condition. Differences between treatment effects for pairs of inducing conditions were considered log2-transformed fold changes (Wolfinger, et al., 2001). Genes were selected for further evaluation if they possessed a p-value <0.004 (corresponding to the significance of difference for SMG1).
|
| |
|
| Submission date |
Aug 31, 2009 |
| Last update date |
Sep 03, 2009 |
| 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) |
| GSE17887 |
Effect of Nrg1 on pathogenesis of Cryptococcus neoformans |
|
