|
| Status |
Public on Aug 07, 2023 |
| Title |
Cauris8973_dsbiofilm_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
NCPF8973
|
| Organism |
[Candida] auris |
| Characteristics |
cell line: NCPF8973
cell type: Dry-surface biofilm
genotype: WT
treatment: Untreated
|
| Growth protocol |
Cells were standardised to 1x106 cells/mL in RPMI-1640 (5% foetal calf serum), seeded into wells of a 24-well plate and incubated at RT for 48 hr. Biofilms were grown by alternating cycles of media on for 48 hr, then media off for 48 hr, for 12 days total.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells and biofilm samples using the RiboPure Yeast Kit (Invitrogen), as per manufacturer's instructions
Libraries were prepared using the Novogene PT042 NGS RNA Library Prep Set (Novogene Ltd) and processed as per Novogene standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Column 8
|
| Data processing |
fastq files were pseudoaligned to the Candida auris B8441 reference genome (version s01-m01-r31), using the quant fuction from the Kallisto package (v0.48.0)
tsv files resulting from the pseudoalignments were summarised to genes using the tximport function from the TxImport package (v1.28.0)
Expression count data were converted to a DGEList, log2-cpm calculated, and data were normalised and filtered using EdgeR (v3.42.4)
Assembly: Candida auris B8441 reference genome (version s01-m01-r31 from Candida Genome Database)
Supplementary files format and content: Tab-delimited text file containing raw count data for each sample
Supplementary files format and content: Tab-delimited text file containing normalised, log-2 transformed counts per million for all samples.
|
| |
|
| Submission date |
Aug 02, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Alicia Ann Ware |
| E-mail(s) |
ware.alicia.a@gmail.com, alicia.ware@gcu.ac.uk
|
| Organization name |
Glasgow Caledonian University
|
| Department |
Biological & Biomedical Sciences
|
| Lab |
Kean Lab
|
| Street address |
Cowcaddens Rd
|
| City |
Glasgow |
| ZIP/Postal code |
G4 0BE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL28368 |
| Series (1) |
| GSE239851 |
Understanding environmental and biocide survival of Candida auris through transcriptional profiling |
|
| Relations |
| BioSample |
SAMN36797586 |
| SRA |
SRX21221704 |
