|
| Status |
Public on Jul 10, 2024 |
| Title |
C_auris_Control-5 |
| Sample type |
SRA |
| |
|
| Source name |
fungal cells
|
| Organism |
[Candida] auris |
| Characteristics |
tissue: fungal cells
genotype: Isolate 12
treatment: untreated
|
| Treatment protocol |
Strains were pre-cultured in YPD broth overnight at 37 °C, diluted to an OD640 of 0.1 in YPD broth (20 mL aliquots in 100 mL Erlenmeyer flasks). Cultures were incubated at 37 °C and 140 rpm for 6 h. HSL (100 or 200 μM final concentration) was added after 4 h of incubation to the exponentially growing phase cultures. Samples were collected after 2 h HSL exposure then were washed three times with physiological saline. Total RNA was isolated from lyophilized fungal cells in three biological replicates.
|
| Growth protocol |
The C. albicans SC5314 reference strain and C. auris isolate 12 (NCPF 8973), derived from the South Asian/Indian lineage, were used in this study. Both strains were maintained on YPD agar plates [YPD broth (VWR, 1% yeast extract, 2% peptone, 2% glucose) and 2% agar (VWR), pH 5.8)] at 37 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441 and C. albicans SC5314.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: genome: https://fungi.ensembl.org/_candida_auris_gca_002759435/Info/Index; features: http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes p , corrected p. fold change, log fold change values and raw data for each Samples
|
| |
|
| Submission date |
Jul 05, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Agnes Jakab |
| E-mail(s) |
jakab.agnes@med.unideb.hu
|
| Organization name |
University of Debrecen
|
| Street address |
Nagyerdei krt 98.
|
| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL24811 |
| Series (1) |
| GSE271513 |
Comparative physiologycal and transcriptome analysis of Candida auris and Candida albicans to exogenous homoserine-lactone |
|
| Relations |
| BioSample |
SAMN42332021 |
| SRA |
SRX25215414 |
