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| Status |
Public on Mar 16, 2022 |
| Title |
1184/P/13-R_R2 |
| Sample type |
SRA |
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| Source name |
fungal cells
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| Organism |
[Candida] auris |
| Characteristics |
genotype: clinical isolate: 1184/P/13-R
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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 |
SAMN26580202 |
| SRA |
SRX14437343 |
| 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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