|
| Status |
Public on Apr 01, 2021 |
| Title |
dinorΔ Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
C. auris
|
| Organism |
[Candida] auris |
| Characteristics |
genotype: CBS10913 leu2[delta]:FRT arg4:PB[LEU2] dinor[delta]:FRT
treatment: Untreated
|
| Growth protocol |
Overnight cultures were diluted 1:100 into 50 mL of YPD medium and grown at 30 °C with shaking for 18 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.5 and processed by Trim Galore version 0.4.4 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the STAR version 020201 and Subjunc version 1.5.3 software.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). The GO term analysis of biological processes represented in DEGs was performed using clusterProfiler version 3.10.1.
Genome_build: C. auris B8441 (GCA_002759435.2)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Mar 31, 2021 |
| Last update date |
Apr 02, 2021 |
| Contact name |
Yabing Song |
| E-mail(s) |
songyb0519@gmail.com
|
| Organization name |
Tsinghua University
|
| Street address |
Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL28368 |
| Series (1) |
| GSE171261 |
Identification of the lncRNA DINOR as a global stress regulator in the super fungus Candida auris |
|
| Relations |
| BioSample |
SAMN18577976 |
| SRA |
SRX10489761 |
