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Sample GSM5049599 Query DataSets for GSM5049599
Status Public on Jan 30, 2021
Title 470147_repl1
Sample type SRA
 
Source name 470147_fungal cells
Organism [Candida] auris
Characteristics genotype/clinical isolate: 470147
treatment: none
Extracted molecule total RNA
Extraction protocol Total RNA was purified using Genejet RNA purification kit (Thermo Scientific). Quality of RNA was assessed on a Bioanalyzer using the RNA6000 Nanochip (Agilent), mRNA was enriched using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.
The qualified libraries were subjected to Illumina sequencing with a 75 bp paired-read length at the Novogene (Novogene, USA) sequencing facility.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 470147_A_S4
Data processing The quality of raw reads were analyzed using FastQC (Andrews, 2010)⁠.
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to C. auris genome (B11221 GCF_002775015.1) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT). Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B11221 (settings: -f bam -t gene -i ID).
Differential gene expression analysis was done using pair-wise comparisons in edgeR (Robinson et al., 2009)
Genome_build: C. auris genome (B11221 GCF_002775015.1)
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
 
Submission date Jan 29, 2021
Last update date Jan 31, 2021
Contact name Sabrina Jenull
E-mail(s) sabrina.jenull@univie.ac.at
Organization name Max Perutz Labs
Lab Kuchler
Street address Dr. Bohrgasse 9/2
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL29671
Series (1)
GSE165762 Transcriptional Signatures Predict Phenotypic Variations of Candida auris
Relations
BioSample SAMN17674194
SRA SRX9975057

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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