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Sample GSM7427909 Query DataSets for GSM7427909
Status Public on Dec 11, 2023
Title Tyrosol-1
Sample type SRA
 
Source name fungal cells
Organism [Candida] auris
Characteristics tissue: fungal cells
genotype: Isolate 12
treatment: Tyrosol treated
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 SAMN35365696
SRA SRX20516514

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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