|
| Status |
Public on Aug 25, 2020 |
| Title |
DA3 |
| Sample type |
SRA |
| |
|
| Source name |
cultures
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
developmental stage: Biofilm
treatment: arachidonic acid (dissolved in EtOH) and DMSO
|
| Treatment protocol |
Biofilms were treated differently with arachidonic acid (dissolved in EtOH) and DMSO; fluconazole (dissolved in DMSO) and EtOH; fluconazole (dissolved in DMSO) and arachidonic acid (dissolved in EtOH) and DMSO and EtOH.
|
| Growth protocol |
Preculture of Candida albicans SC5314 in yeast nitrogen base was grown under biofilm forming conditions in RPMI medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy protect mini kit (Qiagen), while the DNA present was removed with RNase-Free DNase Set (Qiagen). For the preparation of sequencing library, ribosomal RNA was removed from 1 µg of RNA per sample, using the Illumina Ribo-zero rRNA removal kit, and purified with an Agencourt RNAClean XP kit.
Indexed libraries were prepared using the ScriptSeqTM v2 RNA-Seq Library Preparation Kit and ScriptSeqTM Index PCR Primers-Set 1 (Illumina). The library size was profiled with the Bioanalyzer High Sensitivity Assay Kit (Agilent) and quantified with the Qubit HS DNA Assay Kit. The samples were diluted and spiked with a Phix control library (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DMSO_Ethanol_and_DMSO_AA.xlsx
DEvsDA.xlsx
|
| Data processing |
Quality of sequences was analysed with FastQC v0.11.5
Low quality reads (<Q30) were discarded using PRINSEQ-lite v0.20.4
Sequences were aligned using TopHat2 v2.2.1 modified with fr-secondstrand, -r 250 mate-std- I 10000 -G option (Dutton et al., 2016), which gave a much better alignment rate.
Gene expression count tables were built from BAM files, created with TopHat2 using the BEDTools multicov command
Counts were used to evaluate the differential expression of genes with DESeq2; Cuffdiff was also used to generate differential expression data using aligned reads obtained from TopHat2 which were assembled with Cufflinks and merged with Cuffmerge.
Genome_build: C. albicans SC5314 genome assembly 21 (Skrzypek et al., 2017)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample for Cuffdiff and a count table for DESeq2
|
| |
|
| Submission date |
Sep 13, 2019 |
| Last update date |
Aug 25, 2020 |
| Contact name |
Oluwasegun Olalekan Kuloyo |
| E-mail(s) |
skuloyo@gmail.com, 2010109961@ufs4life.ac.za
|
| Phone |
+27(0)514017483
|
| Organization name |
University of the Free State
|
| Department |
Microbial Biochemical and Food Biotechnology
|
| Lab |
Pathogenic Yeast
|
| Street address |
200 Nelson mandela drive, Park west
|
| City |
Bloemfontein |
| State/province |
9300 |
| ZIP/Postal code |
9301 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE137423 |
Transcriptome Analysis of Candida albicans Biofilms Grown in the Presence of Arachidonic Acid and Fluconazole |
|
| Relations |
| BioSample |
SAMN12746275 |
| SRA |
SRX6847379 |
