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| Status |
Public on May 02, 2022 |
| Title |
AmBR1 rep3 |
| Sample type |
SRA |
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| Source name |
Clinical isolate
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| Organism |
[Candida] auris |
| Characteristics |
phenotype: AmB-resistant
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| Growth protocol |
Overnight-grown C. auris cultures were inoculated into YPD (initial OD600 of 0.1) and grown at 30°C for 4h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Genejet RNA purification kit (Thermo Scientific).
mRNA was enriched using oligo(dT) beads (NEB), and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.
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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 |
Raw reads from RNA-seq libraries were filtered to remove the adaptor sequences, low-quality reads (the quality value of over 50% bases of the read is ≤ 20), and the reads containing N > 0.1% (N represents base that could not be determined).
C. auris B8441 reference genome was downloaded from Candida Genome Database (http://www.candidagenome.org) and mapped to the clean reads using HISAT2
HTSeq was used to count the read numbers mapped for each gene. The FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the gene read counts mapped.
Read count obtained from gene expression analysis was used to do differential expression analysis using the DESeq2 R package, while the significant criterion is false discovery rate (padj) <0.05 and log2 fold change ≥0.585.
For further downstream analysis, C. albicans orthologs were retrieved from the Candida Genome Database (http://www.candidagenome.org).
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: Fold change in gene expression in AmB resistant strains compared to susceptible strain
Genome_build: C. auris B8441 reference genome
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| Submission date |
Dec 14, 2021 |
| Last update date |
May 02, 2022 |
| Contact name |
Neeraj Chauhan |
| Organization name |
NJMS-PHRI
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| Department |
Department of Microbiology, Biochemistry & Molecular Genetics
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| Lab |
Neeraj chauhan
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| Street address |
225 Warren Street
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| City |
NEWARK |
| State/province |
New Jersey |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL28368 |
| Series (1) |
| GSE190920 |
Comparative Transcriptomics Reveal Determinants of Amphotericin B Resistance in Candida auris |
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| Relations |
| BioSample |
SAMN24040622 |
| SRA |
SRX13438120 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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