|
| Status |
Public on Jan 20, 2024 |
| Title |
57055_R+S_3 |
| Sample type |
RNA |
| |
|
| Source name |
Filamentous cells
|
| Organism |
Candida albicans |
| Characteristics |
cell type: Filamentous cells
genotype: Clinical strain
growth condition: 37 degree _ R + S (10%)
|
| Growth protocol |
For in vitro filament induction, C. albicans strains were inoculated overnight at 30C in YPD media, harvested, and diluted into RPMI + 10% Serum at a 1:50 ratio and incubated for 4 hours at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For in vitro filament induction samples, after 4hr induction at 37 degree celsius , cells were collected and RNA was extracted according to the manufacturer protocol for MasterPure Yeast RNA Purfification Kit
For in vivo C. albicans cells, after 24 hours post injections, mouse was euthanized and infected ear was excised and the total RNA was extracted using first Trizol method followed by Qiagen RNeasy kit
|
| Label |
none
|
| Label protocol |
N/A
|
| |
|
| Hybridization protocol |
Default nCounter Sprint Profiler Protocol
|
| Scan protocol |
Samples were processed on a nCounter Digital Analyzer
|
| Data processing |
RCC files for each sample were imported into nSolver software to determine the quality control metrics. Using the negative probe set the background values were defined and use as a background threshold and this value is subtracted from the raw counts. The resulting background subtracted total raw RNA counts were first normalized against the highest total counts from the biological triplicates and then to the highest total counts for the samples. The statastical significance of changes in gene expression was determined using Benjamini-Hochberg method at an FDR of 0.1
Background subtracted counts were normalized against the highest total counts from the biological replicates.
The resulting values were then averaged and further normalized to highest counts for the samples
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
Jan 20, 2024 |
| Contact name |
Rohan S. Wakade |
| E-mail(s) |
rwakade@uiowa.edu
|
| Organization name |
University of Iowa
|
| Department |
Department of Pediatrics
|
| Street address |
25, South Grand Avenue, 2020 MedLabs, Department of Pediatrics
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL34110 |
| Series (1) |
| GSE253732 |
The role of the C. albicans transcriptional repressor NRG1 during filamentation and disseminated candidiasis is strain-dependent |
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