|
| Status |
Public on Dec 31, 2024 |
| Title |
WT_Mn_5min R1 |
| Sample type |
SRA |
| |
|
| Source name |
SN148-CIp20
|
| Organism |
Candida albicans |
| Characteristics |
cell line: SN148-CIp20
cell type: Yeast cells
genotype: WT
treatment: 90 min in SC+MN
|
| Treatment protocol |
Cultures were then either left untreated or exposed to 1 mM MnCl2 and incubated at 30°C for 5 and 90 min. For RNA-seq profiling of Mn excess, overnight cultures of WT cells were diluted to an OD600 of 0.1 in fresh 100 ml YPD and incubated with shaking at 30°C to an OD600 of 0.8 and split into 50-ml cultures. MnCl2 was added to the experimental culture to a final concentration of 7.5 mM, while an equal volume of sterile water was added to the control culture and incubated for 30 min. Cells were harvested by centrifugation and were quick-frozen and stored at -80°C.
|
| Growth protocol |
Overnight cultures of WT (SN148-CIp20) strain and smf12 mutant were diluted to an OD600 of 0.1 in 60 ml of fresh SC-Mn medium and grown at 30°C under agitation (200 rpm) to early logarithmic phase (OD600=0.4).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater
The NEBNext UltraTM II RNA Library Prep Kit for Illumina was used to construct the RNA-seq library following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: WT_Mn_5min_R1
|
| Data processing |
Sequencing reads were filtered with fastp version 0.23.2
Filtered reads were mapped to the reference genome sequence of strain SC5314 with STAR version 2.7.9a
The number of reads mapping on each of the genes was calculated by featurecount version 2.0.1
Differential gene expression was calculated with DESeq2 version 1.26.0.
Assembly: GCF_000182965.3
Supplementary files format and content: Tab-delimited file with normalized read counts for each sample
|
| |
|
| Submission date |
Dec 10, 2024 |
| Last update date |
Dec 31, 2024 |
| Contact name |
Adnane Sellam |
| E-mail(s) |
[email protected]
|
| Organization name |
University Laval
|
| Street address |
2705 Laurier Blvd.
|
| City |
Quebec city |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL28323 |
| Series (1) |
| GSE283948 |
Manganese homeostasis modulates glucan and chitin unmasking in Candida albicans |
|
| Relations |
| BioSample |
SAMN45436789 |
| SRA |
SRX27028768 |
