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Sample GSM7008599 Query DataSets for GSM7008599
Status Public on Jul 31, 2023
Title Control-2.
Sample type SRA
 
Source name fungal cells
Organism [Candida] auris
Characteristics tissue: fungal cells
strain: Isolate 12
treatment: untreated
Treatment protocol 15 mM tyrosol treated and untreated exponentially growing phase cultures
Growth protocol YPDA medium (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6)., 140 rpm, 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
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 values, p values, fold change values and raw data for each Sample
 
Submission date Jan 29, 2023
Last update date Jul 31, 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)
GSE223953 Total transcriptome analysis of Candida auris planktonic cells exposed to tyrosol
Relations
BioSample SAMN32953584
SRA SRX19210379

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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