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| Status |
Public on Jan 30, 2021 |
| Title |
470147_repl2 |
| Sample type |
SRA |
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| Source name |
470147_fungal cells
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| Organism |
[Candida] auris |
| Characteristics |
genotype/clinical isolate: 470147
treatment: none
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
470147_B_S5
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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 (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)
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| Submission date |
Jan 29, 2021 |
| Last update date |
Jan 31, 2021 |
| 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 |
GPL29671 |
| Series (1) |
| GSE165762 |
Transcriptional Signatures Predict Phenotypic Variations of Candida auris |
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| Relations |
| BioSample |
SAMN17674193 |
| SRA |
SRX9975058 |
| 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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