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Sample GSM6735377 Query DataSets for GSM6735377
Status Public on Nov 15, 2023
Title ubr2Δ, rep3
Sample type SRA
 
Source name ubr2[delta]
Organism [Candida] auris
Characteristics strain: ubr2[delta]
genotype: CBS10913 leu2[delta]:FRT ubr2[delta]:LEU2
treatment: Untreated
Extracted molecule total RNA
Extraction protocol Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). CGD Gene Ontology Term Finder (http://www.candidagenome.org/cgi-bin/GO/goTermFinder).
Assembly: C. auris B8441 (GCA_002759435.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
 
Submission date Nov 16, 2022
Last update date Nov 15, 2023
Contact name Yabing Song
E-mail(s) songyb0519@gmail.com
Organization name Tsinghua University
Street address Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL28368
Series (1)
GSE218140 The transcription factor Rpn4 activates its own and efflux pumps’ expression to confer fluconazole resistance in Candida auris
Relations
BioSample SAMN31760215
SRA SRX18289028

Supplementary file Size Download File type/resource
GSM6735377_ubr2_Rep3.counts.txt.gz 25.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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