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Status |
Public on Mar 16, 2022 |
Title |
513/P/14_R1 |
Sample type |
SRA |
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Source name |
fungal cells
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Organism |
Candidozyma auris |
Characteristics |
genotype: clinical isolate: 513/P/14
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Growth protocol |
Cells were grown to the logarithmic growh phase in YPD at 30 °C.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was purified using GeneJET RNA purification kit (Thermo Scientific). 5μg DNase-treated total RNA was subjected to mRNA was enrichment 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Htseq_read_counts.txt
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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 (B8441) 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 B8441 (settings: -f bam -t gene -i ID). Assembly: Differential gene expression analysis was done using the glm approach in edgeR (Robinson et al., 2009) Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
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Submission date |
Mar 11, 2022 |
Last update date |
Mar 16, 2022 |
Contact name |
Sabrina Jenull |
E-mail(s) |
sabrina.jenull@univie.ac.at
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Organization name |
Max Perutz Labs
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Lab |
Kuchler
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Street address |
Dr. Bohrgasse 9/2
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City |
Vienna |
ZIP/Postal code |
1030 |
Country |
Austria |
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Platform ID |
GPL28368 |
Series (1) |
GSE198410 |
Transcriptomics and phenotyping define signatures associated with echinocandin resistance in Candida auris |
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Relations |
BioSample |
SAMN26580194 |
SRA |
SRX14437351 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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