NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7476303 Query DataSets for GSM7476303
Status Public on Mar 01, 2024
Title UACa20 grown in Sabouraud's Dextrose, 2
Sample type SRA
 
Source name UACa20
Organism [Candida] auris
Characteristics cell line: UACa20
cell type: Yeast
genotype: WT
treatment: Sabouraud's Dextrose
Treatment protocol Cells grown for 16 hours in specified medium to form aggregates or single cells
Extracted molecule total RNA
Extraction protocol Cells were homogenised in TRIazole (Invitrogen) by bead beating. RNA was isolated by addition of chloroform and isopropanol precipitation. Remaining DNA was removed by RNase-Free DNase kit (Qiagen) following manufacturer's protocols. RNA was cleaned further by using the RNeasy Mini Kit (Qiagen) following manufacturer's protocols.
External RNA Controls Consortium spike-in controls were added to samples before library preperation with Illumina TruSeq Stranded mRNA kit (Illumina Inc.) following the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Phenotype Displayed: Aggregation
2_S2
Data processing Quality of sequencing data and read was analysesd by FastQC (version 0.11.8), TrimGalore! (version 0.6.4) was used to remove low quality reads and adaptor content, with phred quality score threshold of 30.
Genome (Cand_auris_B11221_V1) and annotation file were prepeard for use with HISAT2. Reads were aligned to this reference by HISAT2 using stranded library preparation.
SAMtools was used to process the alignments and reads at gene locations counted by featureCounts (part of the sub read version 1.6.2 package) utilising the parameter to split multi-mapped reads as a fraction across all genes that they align to, with the parameter for stranded analysis.
edgeR (version 3.30.3) was used to detect which genes had a significant differential change in expression. All genes that had a CPM (count per million) value of more than one in three or more samples were kept for analysis, and all other genes were removed as low count genes
Assembly: Cand_auris_B11221_V1
 
Submission date Jun 14, 2023
Last update date Mar 01, 2024
Contact name Centre for Genome-Enabled Biology and Medicine on behalf of listed contributors
Phone +44 (0)1224273471
Organization name University of Aberdeen
Department CGEBM
Street address 23 St Machar Drive
City Aberdeen
State/province Aberdeenshire
ZIP/Postal code AB24 3RY
Country United Kingdom
 
Platform ID GPL24811
Series (1)
GSE234899 Differential gene expression of gene during media induced aggregation
Relations
BioSample SAMN35732646
SRA SRX20676310

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap