|
| Status |
Public on Jul 05, 2021 |
| Title |
QMY23+BM_1 |
| Sample type |
SRA |
| |
|
| Source name |
QMY23 fungal cells
|
| Organism |
Candida albicans |
| Characteristics |
strain: QMY23
genotype: wild type
treatment: BM
|
| Treatment protocol |
The pre-cultures were diluted to 0.1 OD640 in YPD ± 2 mM BM then were grown at 37 ºC. MSB was added in the final concentration of 1.5 mM at 4 h incubation time. Fungal cells were collected after 5 h inoculation (at 1 h following MSB stress treatment) by centrifugation (5 min of 4000 × g at 4°C).The cells were washed three times with phosphate-buffered saline (PBS) and stored at -70°C until use.
|
| Growth protocol |
The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The yeast pre-cultures were grown in 5 ml YPD medium at 37 ºC for 18 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freeze- lyophilized cells were processed using TRISOL (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop and capillary electrophoresis.
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. The single read 75 bp long sequencing reads were generated on Illumina NextSeq500 instrument. Approximately 16–36 million reads per samples were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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.
Tophat (version 2.1.1) and Bowtie (version 2.3.4.1) bioinformatics tools were used for the mapping and generating bam files, and htseq-count (from “HTSeq” framework, version 0.6.1p1) to generate read counts of A and B alleles.
The read counts of the corresponding A and B alleles were merged and these merged values were used for differential expression analysis using DESeq2 (version 1.24.0)
Genome_build: C. albicans SC5314 (candida genome database; Genome: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/archive/C_albicans_SC5314_version_A22-s07-m01-r85_chromosomes.fasta.gz, features: http://www.candidagenome.org/download/gff/C_albicans_SC5314/archive/C_albicans_SC5314_version_A22-s07-m01-r85_features_with_chromosome_sequences.gff.gz)
Supplementary_files_format_and_content: RNAseq.xlsx (Excel file includes row counts data for A and B alleles)
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Jul 05, 2021 |
| Contact name |
Agnes Jakab |
| E-mail(s) |
jakab.agnes@med.unideb.hu
|
| Organization name |
University of Debrecen
|
| Street address |
Nagyerdei krt 98.
|
| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE173668 |
The Negative Effect of Protein Phosphatase Z1 Deletion on the Oxidative Stress Tolerance of Candida albicans Is Synergistic with Betamethasone Exposure |
|
| Relations |
| BioSample |
SAMN18939887 |
| SRA |
SRX10723929 |
