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| Status |
Public on Jan 12, 2019 |
| Title |
SNP rep1 |
| Sample type |
SRA |
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| Source name |
whole cells
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| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
genotype: wild-type
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| Treatment protocol |
Addition of 1mM SNP, 0.5 mM SHAM, or 1 mM SNP+ 0.5 mM SHAM, 30 °C shaking incubation for 30 min, followed by RNA extraction
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| Growth protocol |
Inoculation of YPD with overnight cultures to final OD600 nm of 0.2, followed by 5 h shaking incubation 30 °C
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| Extracted molecule |
total RNA |
| Extraction protocol |
E.Z.N.A.® Yeast RNA Kit (Omega Bio-tek, Norcross, GA) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
untreated vs SNP.txt
wild-type treated with SNP
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| Data processing |
Illumina NextSeq500 used for basecalling
Sequence quality was assessed using FASTQC. No trimming was performed
Each raw fastq data file was used to map reads to Assembly 21 of C. albicans SC5314 using HISAT2 v1.01. BAM files for technical replicates were merged using Picard (Galaxy version 1.1.2), in order to generate a single BAM file for each biological replicate
Gene differential expression testing was performed to compare groups using three biological replicates each, using Cuffdiff v. 2.2.1.1. with the following parameter changes from default: multi-read correction: yes, perform bias correction: yes (C. albicans SC5314 genome Assembly 21)
Genome_build: C. albicans SC5134 Assembly 21
Supplementary_files_format_and_content: Tab-delimited test files Cuffdiff output for gene differential expression testing comparing untreated sample group ("WT") with each other sample group. Including FPKM, log2(fold_change), test_stat, p value, q-value
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| Submission date |
May 16, 2018 |
| Last update date |
Jan 12, 2019 |
| Contact name |
Lucian Duvenage |
| Organization name |
University of Kent
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| Department |
School of Biosciences
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| Street address |
Giles Lane
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| City |
Canterbury |
| ZIP/Postal code |
CT2 7NJ |
| Country |
United Kingdom |
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| Platform ID |
GPL22403 |
| Series (1) |
| GSE114531 |
Transcriptomes of wild-type C. albicans treated with respiration inhibitors SNP, SHAM or SNP+SHAM |
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| Relations |
| BioSample |
SAMN09213778 |
| SRA |
SRX4089490 |
| 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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