|
| Status |
Public on Jun 28, 2017 |
| Title |
T1_nt_r2 |
| Sample type |
SRA |
| |
|
| Source name |
Untreated for 1 h
|
| Organism |
Candida albicans |
| Characteristics |
strain: SC5314
exposure time: 1h
|
| Treatment protocol |
Fifty µl of solvent (DMSO) or 250 µM tomatidine (diluted in DMSO) were added to the culture to reach a concentration 1% DMSO and 2.5 µM tomatidine
|
| Growth protocol |
Overnight YPD culture of C. albicans SC5314 strain was diluted 1:200 in 5 ml YPD media and incubated under agitation at 30° C until early exponential growth phase (OD540 = 0.3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted after 1 h or 3 h tomatidine/solvent exposure by mechanical disruption of the cells with glass beads. Experiments were carried out in triplicates with 12 samples
Total RNA extracts were treated with DNase using the DNA-free kit (Ambion-Life Technologies, Zug, Switzerland) and RNA quality and integrity was verified with Fragment Analyzer™ Automated CE System (Advanced Analytical). One µg of RNA was used to create sequencing libraries through standard Illumina TruSeq stranded mRNA protocol. Each library (sample) received a different index enabling several libraries to be multiplexed. Before RNA sequencing, libraries were analyzed with a fragment analyzer to assess quality and fragment size and with a Qubit fluorometer (Invitrogen) to determine cDNA concentration. Libraries were kept at −20°C until sequencing. The 12 libraries were run on Illumina HiSeq platerform (HiSeq2500)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing data were processed using Illumina Pipeline software. Reads were filtered, trimmed, and counts align to the SC5314 C. albicans reference genome using CLC workbench pipeline. The numbers of read counts per gene locus was extracted
Data normalization and gene expression analysis were performed in R (v3.2.3), using Bioconductor packages. The read count data were normalized using TMM (trimmed mean of M-values) method available in the R package edgeR and transformed into log2 counts per million by Voom method from R package Limma. This package was then used to apply a linear model with one factor per condition (4 conditions: untreated 1h, tomatidine-treated 1h, untreated 3h, tomatidine-treated 3h (all in triplicates)) to the transformed data. Two contrasts representing the difference between tomatidine-treated and untreated cells at each drug exposure time (1- and 3 h) were extracted from the linear model to result in a moderated t statistic for all genes expressed.
Genome_build: SC5314 C. albicans reference genome
Supplementary_files_format_and_content: Excel data sheets; Gene counts, Voom normalized gene expression, 1- and 3-h tomatidine treatment
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dominique Sanglard |
| E-mail(s) |
Dominique.Sanglard@chuv.ch
|
| URL |
http://www.chuv.ch/imul
|
| Organization name |
University of Lausanne and University Hospital Center
|
| Street address |
Rue Bugnon 48
|
| City |
Lausanne |
| ZIP/Postal code |
1011 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19036 |
| Series (1) |
| GSE96965 |
Identification and mode of action of a plant natural product targeting human fungal pathogens |
|
| Relations |
| BioSample |
SAMN06630326 |
| SRA |
SRX2663909 |
