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| Status |
Public on Dec 20, 2021 |
| Title |
ksb005_S81_upc2A∆ |
| Sample type |
SRA |
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| Source name |
Exponential phase growth yeast cells
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| Organism |
Nakaseomyces glabratus |
| Characteristics |
genotype: upc2A_delta
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| Growth protocol |
Growth in YPD to exponential phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected via centrifugation from growth medium and RNA harvested according to manufacturer protocol for MasterPure Yeast RNA Purification Kit
Libraries were prepared with paired end adapters using Illumina chemistries per manufacturer’s instructions, and sequencing of libraries were performed with read lengths of approximately 150bp with at least 50 million reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
ksb005
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| Data processing |
Read quality was confirmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the Candida glabrata CBS138 genome using HISAT2 in paired-end read mode. Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat Biotechnol 37, 907–915 (2019). Sorted and indexed bam files of mapped reads were prepared using Samtools (https://www.htslib.org). Mapped reads were assembled onto annotated CBS138 genes with Stringtie using the -eB parameter and raw gene count tables were generated using the prepDE.py script that is provided with Stringtie. Pertea M., Kim D., Pertea G.M., Leek J.T., Salzberg S.L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016). Differential expression and statistical analysis were done from raw counts using the DESeq2 R package. The default negative binomial general linear model and Wald test were used. Correction for multiple hypothesis tests was done using the default Benjamini and Hochberg method. Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550 (2014).
Genome_build: s03-m01-r23 from Candida Genome Database on 2021 July 11
Supplementary_files_format_and_content: matrix table with relative abundance measurements to wild type
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| Submission date |
Dec 17, 2021 |
| Last update date |
Dec 20, 2021 |
| Contact name |
Damian J Krysan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Iowa Hospitals and Clinics
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| Department |
Division of Pediatrics & Infectious Disease
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| Lab |
Krysan
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| Street address |
25 South Grand, 2040 ML
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| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platform ID |
GPL31108 |
| Series (1) |
| GSE191145 |
Loss-of-function ROX1 mutations suppress the fluconazole susceptibility of upc2A∆ mutation in Candida glabrata, implicating additional positive regulators of ergosterol biosynthesis |
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| Relations |
| BioSample |
SAMN24171463 |
| SRA |
SRX13441253 |
| 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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