|
| Status |
Public on Jan 01, 2024 |
| Title |
cyc1K79A Yeast-1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cell
|
| Organism |
Candida albicans SC5314 |
| Characteristics |
tissue: Whole cell
strain: SC5314
cell type: Yeast cell
genotype: cyc1K79A
treatment: Yeast culture
|
| Treatment protocol |
Overnight yeast cultures were diluted (1 :20) to fresh YPD medium containing 10% fetal bovine serine (FBS) and incubation at 37°C for 1-2 h.
|
| Growth protocol |
C. albicans strains were grown in YPD at 30°C overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Trizol reagent according to the manufacturer’s instructions (Invitrogen).
RNA-seq transcriptome library was prepared from 1 mg of total RNA using Illumina’s TruSeq RNA sample preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
R11946
|
| Data processing |
The raw paired-end reads were trimmed using SeqPrep.
The raw paired-end reads were quality-controlled using Sickle.
The clean reads were mapped to C. albicans reference genome SC5314 (assembly ASM18296v3) using the STAR aligner (version 2.2.1)
Mapped reads were summarized to the gene level with the featureCounts software (version 1.6.3).
Gene differential analysis was done using the Bioconductor R package edgeR in R (version 3.6.2).
Assembly: C. albicans reference genome SC5314 (assembly ASM18296v3)
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text files include RPKM value for each sample
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Guisheng Zeng |
| E-mail(s) |
zeng_guisheng@idlabs.a-star.edu.sg
|
| Organization name |
Agency for Science, Technology and Research
|
| Department |
Infectious Diseases Labs
|
| Lab |
WY
|
| Street address |
8A Biomedical Grove, #05-13 Immunos Building, Immunos
|
| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL33780 |
| Series (1) |
| GSE243813 |
Unmethylated Cyc1 downregulates hyphal specific genes and upregulates hyphal suppressors in Candida albicans |
|
| Relations |
| BioSample |
SAMN37516828 |
| SRA |
SRX21861169 |
