|
| Status |
Public on Oct 06, 2024 |
| Title |
PLC124 Fluconazole R1 |
| Sample type |
SRA |
| |
|
| Source name |
Clinical isolate; fluconazole resistant
|
| Organism |
Candida albicans |
| Characteristics |
cell type: Clinical isolate; fluconazole resistant
genotype: PLC124
treatment: Fluconazole 1 ug/ml
|
| Treatment protocol |
The starting culture was split into two tubes (2 mL per tube) and subsequently grown at 30 °C aerated until an OD600 of 1.5 – 2.2. One tube was treated with 2% DMSO (diluent control), while the second tube was treated for 30 minutes with 1 μg/ml (1x MIC (24)) fluconazole.
|
| Growth protocol |
C. albicans reference strain SC5314 and fluconazole resistant clinical isolate PLC124 were maintained on YPD (yeast extract 1%, peptone 2%, and glucose 2%). cultures were pre-grown overnight at 30 °C with constant shaking. The following day cultures were diluted to OD600 of 0.1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen cell pellets using the RiboPure-Yeast RNA Isolation Kit (Thermo Fisher) and RNA concentrations were measured using a Nanodrop 2000c Spectrophotometer (Thermo Fisher Scientific).
Ribosomal RNA was depleted from ~1 µg of total RNA using riboPOOLs (siTOOLs Biotech) kit as recommended by the manufacturer. After depletion samples were precipitated using 2.5 volumes of 95% (vol/vol) ethanol, a 1/10 volume of 3M sodium acetate and 1 µL of glyucoblue, mixed and incubated overnight at -20 °C. Concentration was done by centrifugation at 14000 x g, 30 minutes at 4°C, the pellets were washed twice with 70% ethanol, dried and resuspended.
For library preparation, we used the NEBNext Ultra directional RNA Library Prep kit for Illumina (New England BioLabs) as recommended by the manufacturer for relatively low input,13 amplification cycles, and mean library size was around 350bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RNAseq
|
| Data processing |
After quality control, raw data was mapped to SC5314 reference genome (ASM18296v3) using STAR version 2.7.9a aligner (paired-end), file formats were converted, sorted and indexed using samtools
Assembly: SC5314 reference genome (ASM18296v3)
Supplementary files format and content: Gene count file was generated using Subread featureCounts version 1.5.1 with the option ‘-t CDS’
Supplementary files format and content: tab delimited file containing gene level raw counts
|
| |
|
| Submission date |
May 20, 2024 |
| Last update date |
Oct 06, 2024 |
| Contact name |
Irene Stevens |
| E-mail(s) |
irene.stevens@scilifelab.se
|
| Phone |
0046728774966
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Microbiology, Tumor and Cell Biology
|
| Lab |
Pelechano
|
| Street address |
Tomtebodavägen 23A (Gamma5)
|
| City |
Solna |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL32241 |
| Series (1) |
| GSE267941 |
The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN41464480 |
| SRA |
SRX25986274 |
