|
| Status |
Public on Mar 24, 2013 |
| Title |
Wild type - replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
WT-2 rapa
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
treatment: 0.2 ug/ml rapamycin for 0.5 h
|
| Treatment protocol |
After 4.5 h of incubation, cultures were treated with 0.2 ug/ml rapamycin for 0.5 h.
|
| Growth protocol |
Cell cultures were grown in YPD medium at 30°C overnight and subsequently diluted into fresh YPD medium to an OD600 = 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by the phenol-chloroform method and genomic DNA was removed by TURBO DNase (Ambion, Inc.). Purified RNA was quantified at OD260 using a ND-1000 spectrophotometer (Nanodrop Technology) and qualitated using Bioanalyzer 2100 (Agilent Technology) with RNA 6000 nano labchip kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
For cRNA synthesis, 0.2 ug total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies) and labeled with Cy3 (CyDye, Agilent Technologies)
|
| |
|
| Hybridization protocol |
Total 0.6 ug Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent C_albicans_21 Oligo 8×15K Microarray (Agilent Technologies) at 65°C for 17 h.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3.
|
| Description |
Geneexpression after 0.5 h of rapamycin treatemnt
|
| Data processing |
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies). Normalization and expression analysis was performed by using GeneSpring GX 11.5 (Agilent Technologies). Genes considered to be significantly regulated in hap5-null mutant were based on an average expression level change of ≥ 2-fold to wild type (average ratio of four independent replicates) and the p-value less than 0.05.
|
| |
|
| Submission date |
Oct 01, 2012 |
| Last update date |
Mar 24, 2013 |
| Contact name |
Po-Chen Hsu |
| E-mail(s) |
d9580519@oz.nthu.edu.tw
|
| Organization name |
National Tsing Hua university
|
| Department |
Institute of Molecular and Cellular Biology
|
| Street address |
Room 404, Life Science Building I, No. 101, Section 2, Kuang-Fu Road
|
| City |
Hsinchu |
| ZIP/Postal code |
30013 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL14575 |
| Series (1) |
| GSE41266 |
Comparative analysis between wild type and hap5-null mutant in response to rapamycin treatment |
|
