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Sample GSM5452703

Query DataSets for GSM5452703

Status

Public on Sep 30, 2021

Title

Farnesol_2

Sample type

SRA

Source name

fungal cells

Organism

[Candida] auris

Characteristics

strain: isolate 12
genotype: wild type
agent: Farnesol

Treatment protocol

Following 4 hours incubation time YPD medium was supplemented with a final concentration of 75 μM farnesol and fungal cells were collected 2 hours following farnesol exposure by centrifugation (5 min, RCF=4000×g, 4°C). The cells were washed three times with phosphate-buffered saline and stored at -70°C until use.

Growth protocol

The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 30ºC with 2.3 Hz shaking frequency for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 2.3 Hz shaking frequency.

Extracted molecule

total RNA

Extraction protocol

Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop (ThermoFisher Scientific, Waltham, MA USA) and capillary electrophoresis.
The quality of RNA was determined with the Eukaryotic Total RNA Nano kit (Agilent, USA) using Agilent Bioanalyzer. RNA-Seq libraries were prepared from total RNA using NEBNext Ultra II RNA Sample Preparation kit (NEB, USA) according to the manufacturer’s protocol. The single read 75 bp long sequencing reads were generated on Illumina NextSeq500 instrument. Approximately 18-22 million reads per samples were generated.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Raw reads were aligned to the reference genome
Aligned reads varied between 90-95 % in each sample.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene expression values.
Gene expression 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 (differentially expressed genes).
Genome_build: Genome: „http://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: Exel file includes corrected p values, fold change values, normalized and raw data.

Submission date

Jul 14, 2021

Last update date

Sep 30, 2021

Contact name

Agnes Jakab

E-mail(s)

jakab.agnes@med.unideb.hu

Organization name

University of Debrecen

Street address

Nagyerdei krt 98.