|
| Status |
Public on Dec 11, 2023 |
| Title |
Control-2 |
| Sample type |
SRA |
| |
|
| Source name |
fungal cells
|
| Organism |
[Candida] auris |
| Characteristics |
tissue: fungal cells
genotype: Isolate 12
treatment: untreated
|
| Treatment protocol |
Tyrosol and farnesol in 15 mM and 75 μM concentrations were added to preformed one-day-old biofilms and then the plates were incubated for 24 hours at 37 °C.
|
| Growth protocol |
C. auris isolate was subcultured on YPD agar for 48 hours at 37 °C. Fungal cells were harvested by centrifugation at 3000 × g for 5 min and were washed three times with sterile physiological saline. After the final washing, pellets were re-suspended in physiological saline and the cell density was adjusted to 1 × 10^6 cells/ml in RPMI-1640 media for each experiment using Burker’s chamber. The 550 μl suspensions of C. auris cells were placed on the bottom of 24-well polystyrene plates (TPP, Trasadingen, Switzerland) to 450 μl RPMI-1640 media and reincubated statically for 24 hours at 37 °C. After the incubation time, culture medium was aspired and non-adherent cells were removed by washing the biofilms with sterile physiological saline.
|
| 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
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 log fold change values and raw data for each Sample
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
Dec 11, 2023 |
| 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) |
| GSE233427 |
Comparative transcriptional analysis of Candida auris biofilms following farnesol and tyrosol treatment |
|
| Relations |
| BioSample |
SAMN35365698 |
| SRA |
SRX20516512 |
