|
| Status |
Public on Aug 18, 2012 |
| Title |
wild-type_grown in RPMI medium for 2 hours_biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type grown in RPMI medium for 2 hours
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
treatment: RPMI-grown Candida glabrata cells
genotype/variation: wild-type
|
| Treatment protocol |
After 2 and 10 hr incubation either in RPMI-medium or co-culturing with THP-1 macrophages, yeast cells were collected, washed and lysed with glass beads in trizol.
|
| Growth protocol |
YPD-medium grown overnight cultures of wild-type and mutant Candida glabrata cells were inoculated either in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum or infected to PMA-activated human THP-1 macrophages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using acid phenol extraction method and frozen at -80OC. Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .
|
| Label |
Cy3
|
| Label protocol |
1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented.
|
| |
|
| Hybridization protocol |
With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization cocktail was then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a C. glabrata 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 032958) was placed. This microarray “sandwich” was then sealed in a hybridization chamber. The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours
|
| Scan protocol |
The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1
|
| Data processing |
Data from replicate probes were averaged and mean expression values were subjected to Quantile normalization.
|
| |
|
| Submission date |
Jun 26, 2012 |
| Last update date |
Aug 18, 2012 |
| Contact name |
Rupinder Kaur |
| E-mail(s) |
rkaur@cdfd.org.in
|
| Organization name |
Centre for DNA Fingerprinting and Diagnostics
|
| Department |
Fungal Pathogenesis
|
| Street address |
Building 7, Gruhakalpa,Nampally
|
| City |
Hyderabad |
| State/province |
AP |
| ZIP/Postal code |
500001 |
| Country |
India |
| |
|
| Platform ID |
GPL15745 |
| Series (1) |
| GSE38953 |
Gene expression profiling of RPMI-grown and macrophage-internalized Candida glabrata wild-type, Cgrsc3-a∆ and Cgrtt109∆ cells. |
|
