|
| Status |
Public on Mar 01, 2024 |
| Title |
UACa11 grown in RPMI-1640, 2 |
| Sample type |
SRA |
| |
|
| Source name |
UACa11
|
| Organism |
[Candida] auris |
| Characteristics |
cell line: UACa11
cell type: Yeast
genotype: WT
treatment: RPMI-1640
|
| 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: Non-aggregating
11_S11
|
| 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 |
SAMN35732637 |
| SRA |
SRX20676319 |
