|
| Status |
Public on Oct 11, 2023 |
| Title |
Δckb2,no MMS, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CBS138
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
cell line: CBS138
cell type: Yeast cells
genotype: CgCKB2 knockdown
treatment: untreated
time: 0h
|
| Treatment protocol |
Log-phase cultures of WT , Δckb1 and Δckb2 strains were either treated with 0.01% MMS for 1 h, or left untreated.
|
| Growth protocol |
The WT , Δckb1 and Δckb2 strains were inoculated in YPD media and grown to saturation overnight. Cells were diluted to an OD600 of 0.1 and recovered to log phase for 4 hours shaking at 30°.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by the acid phenol method. Three biological replicates were performed per condition. RNA was frozen at -80℃ and sent to Shanghai Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China) for further sequencing by Illumina novaseq6000 PE150.
RNA libraries for RNA-seq were prepared using Illumina NovaSeq Reagent Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality-filtered RNA-seq reads were aligned to the C.glabrata genome (http://www.candidagenome.org) by STAR software (version 2.7.4).
Gene expressions were obtained and normalized by StringTie (V2.1.2) and DESeq2 (V1.20).
Significantly expressed genes were screened based on a 2-fold cut-off and p-value < 0.05.
Assembly: Candida glabrata CBS138 genome
Supplementary files format and content: tab-delimited text files include gene count values for each Sample
|
| |
|
| Submission date |
May 12, 2023 |
| Last update date |
Oct 11, 2023 |
| Contact name |
Xianwei Wu |
| E-mail(s) |
xiangewy@gmail.com
|
| Phone |
+8618817524095
|
| Organization name |
Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine
|
| Department |
Institute of Respiratory Diseases
|
| Street address |
No.725 South Wanping Road
|
| City |
shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL33385 |
| Series (1) |
| GSE232439 |
RNA-Seq analysis of Candida glabrata wild-type, Δckb1 and Δckb2 mutant in the presence and absence of methyl methanesulfonate (MMS). |
|
| Relations |
| BioSample |
SAMN35066126 |
| SRA |
SRX20314148 |
