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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 15, 2023 |
| Title |
WT, rep2 |
| Sample type |
SRA |
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| Source name |
WT
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| Organism |
Candidozyma auris |
| Characteristics |
strain: WT
genotype: CBS10913
treatment: Untreated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the hisat2 version 2.1.0.
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). CGD Gene Ontology Term Finder (http://www.candidagenome.org/cgi-bin/GO/goTermFinder).
Assembly: C. auris B8441 (GCA_002759435.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
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| Submission date |
Nov 16, 2022 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Yabing Song |
| E-mail(s) |
songyb0519@gmail.com
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| Organization name |
Tsinghua University
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| Street address |
Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL28368 |
| Series (1) |
| GSE218140 |
The transcription factor Rpn4 activates its own and efflux pumps’ expression to confer fluconazole resistance in Candida auris |
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| Relations |
| BioSample |
SAMN31760219 |
| SRA |
SRX18289024 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6735373_WT_Rep2.counts.txt.gz |
25.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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