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| Status |
Public on Nov 04, 2019 |
| Title |
II_KO2_CTRL |
| Sample type |
SRA |
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| Source name |
fungal cells
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| Organism |
Candida albicans |
| Characteristics |
strain: cappz1
genotype: mutant type
tissue: fungal cells
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| Treatment protocol |
Following 4 hours incubation time YPD medium was supplemented with a final concentration of 0.4 mM tert-butyl-hydroperoxide (tBOOH) and fungal cells were collected 1 hours following tBOOH exposure by centrifugation (10 min, RCF=7750g, 4°C). The cells were washed two times with phosphate-buffered saline and stored at -70°C until use.
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| Growth protocol |
The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 37ºC without shaking for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 140 rpm shaking.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent (Chomczynski BioTechniques. 1993; 15:536–7.) and glass beads. RNA concentration and purity were determined using NanoDrop (Thermo Scientific) and by Bioanalyser (Agilent) using Eukaryotic Total RNA Nano Kit according to the manufacturer's protocol.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94°C. First strand cDNA was generated by random priming reverse transcription; double stranded cDNA was generated in a second strand synthesis step. After repairing ends, A-tailing and adapter ligation steps, adapter-ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp-long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSpace.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome and generate BAM files
DESeq algorithm was used to obtain normalized gene expression values (StrandNGS software)
Gene expression differences between treated and control groups were compared by moderated T-test; Benjamini-Hochberg False Discovery Rate was used for multiple testing correction.
Genome_build: C. albicans SC5314 (C_albicans_SC5314/ Assembly22 genome version, downloaded from www.candidagenome.org)
Supplementary_files_format_and_content: Exel file includes RPKM and fold change values
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| Submission date |
Jul 01, 2019 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Krisztina Szabó |
| E-mail(s) |
szabo.krisztina05@gmail.com
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| Organization name |
University of Debrecen
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| Department |
Medical Chemistry
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| Street address |
Egyetem tér
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| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
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| Platform ID |
GPL22403 |
| Series (2) |
| GSE133611 |
Deletion of the fungus specific protein phosphatase Z1 exaggerates the consequences of oxidative stress elicited by tert-butyl-hydroperoxide in Candida albicans (RNAseq data set) |
| GSE134060 |
Deletion of the fungus specific protein phosphatase Z1 exaggerates the consequences of oxidative stress elicited by tert-butyl-hydroperoxide in Candida albicans |
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| Relations |
| BioSample |
SAMN12172996 |
| SRA |
SRX6385641 |
| 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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