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Sample GSM7675467 Query DataSets for GSM7675467
Status Public on Aug 07, 2023
Title Cauris8978_dsbiofilm_rep1
Sample type SRA
 
Source name NCPF8978
Organism Candidozyma auris
Characteristics cell line: NCPF8978
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 11
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) [email protected], [email protected]
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 SAMN36797583
SRA SRX21221707

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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