|
| Status |
Public on Mar 13, 2024 |
| Title |
AmB/LNP sample 3 [H6] |
| Sample type |
SRA |
| |
|
| Source name |
Candida cells
|
| Organism |
[Candida] auris |
| Characteristics |
strain: AR0390
tissue: Candida cells
treatment: Amphotericin 0.5 + Lansoprazole 30 ug/mL
ng/ul: 188.9
a260/a280: 2.11
a260/a230: 2.36
total volume: 40 ul
|
| Treatment protocol |
Candida cells were treated with the tested drugs in RPMI media
|
| Growth protocol |
C. auris was grown on YPD broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exponential C. auris AR0390 in RPMI 1640 medium were treated with DMSO (control), AmB (0.5 µg/ml), LNP (32 µg/ml), or the combination of AmB/LNP in triplicates for 3 hr at 35 °C. Candida cells were collected, washed three times with PBS, and the total RNA was extracted using a RiboPureTM-Yeast Kit (AmBion, AM1926, MA, USA) as per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
150-bp paired-end DNA samples were sequenced using an Illumina NovaSeq6000. Fastp was used to quality-trim reads and eliminate Illumina TruSeq adaptor sequences. Reads were aligned to the C. auris NCBI reference genome version B11221 using STAR aligner (v2.7.10a) The read counts mapped to each gene were counted using FeatureCounts (v2.1). The EdgeR Bioconductor package (v3.16.5) was used to perform the differential expression analysis. The Benjamini-Hochberg method was used to adjust the P-values for multiple testing. The cutoff for the significant differential expression was chosen at a FDR of 0.05. DEGs were annotated by blasting the sequences of identified DEGs versus C. albicans SC5314 Genome Database with an e-value cutoff of 0.01. Cluster Profiler Bioconductor package (v2.4.3) was used to perform Gene Ontology analysis of DEGs. The length of each gene in the related annotation GTF file and the number of reads mapped to each gene were used to generate FPKM values for each gene.
Assembly: C. auris NCBI reference genome version B11221
|
| |
|
| Submission date |
Sep 26, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Tony Hazbun |
| E-mail(s) |
thazbun@purdue.edu
|
| Phone |
7654968228
|
| Organization name |
Purdue University
|
| Department |
Borch Medicinal Chemistry and Molecular Pharmacology
|
| Lab |
HANS 235
|
| Street address |
201 South University Street
|
| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47906 |
| Country |
USA |
| |
|
| Platform ID |
GPL28368 |
| Series (1) |
| GSE244094 |
Lansoprazole interferes with fungal respiration and acts synergistically with amphotericin B against multidrug-resistant Candida auris |
|
| Relations |
| BioSample |
SAMN37548892 |
| SRA |
SRX21897812 |
