|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Aug 28, 2023 |
Title |
BAC317-TSB1a |
Sample type |
SRA |
|
|
Source name |
culture
|
Organism |
Staphylococcus aureus |
Characteristics |
cell type: culture
|
Growth protocol |
S. aureus CBS2016-05 and PS/BAC/317/16/W strains were grown in TSB and PCs at 22-24°C until early stationary phase.
|
Extracted molecule |
total RNA |
Extraction protocol |
The cells of CBS2016-05 and PS/BA/317/16/W from TSB and PCs from early stationary phase were pelleted at 4°C and subjected to RNA extraction using the miRNeasy Mini Kit, following the manufacturer's instructions. To eliminate genomic DNA, the RNA samples from three independent biological replicates were treated with TURBO™ DNase AmbionTM (Thermo Fisher Scientific). Furthermore, the RNA samples from spiked PCs underwent an additional treatment using the MICROBEnrich™ kit (Ambion) to remove eukaryotic RNA. Input total RNA concentration was measured with the Qubit HS RNA assay (Thermo Q32855). RNA quality was assessed on the Fragment analyzer Standard Sensitivity RNA assay (Agilent DNF-472-0500), with RNA Quality Numbers (RQN) above 8.0. DNA libraries were prepared using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina 20040525), using 150ng of input total RNA. Quantification of the libraries was performed with the Qubit Double Stranded DNA HS kit (Thermo Q32854) and ran on the AATI Fragment Analyzer with the High Sensitivity NGS assay (Agilent DNF-486-0500) to verify the size distribution of the template library. The libraries were normalized, pooled, and diluted as required to achieve acceptable cluster density on the NextSeq 500 sequencer (Illumina SY-414-1001). The library pool then underwent 75 Cycle High Output (Illumina 20024906). RNA-seq was using the NexSeq 500 platform (Illumina).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
PS/BAC/317/16/W grown in TSB until early stationary phase
|
Data processing |
Sequence quality control analysis was performed using FastQC and fastp to assess the quality of the reads. Transcript quantification was conducted using Salmon and the reads were aligned to the genome using bowtie2. The 'lfcShrink()' function in DESeq2 was employed for this analysis, which calculates the log2 fold change between the conditions while shrinking the value in cases of high uncertainty in the estimated fold change, often arising from low read counts assigned to the gene. Assembly: Genome sequences of S. aureus CBS2016-05 and PS/BAC/317/16/W. Accession numbers are CP070991.1 and NZ_CP071104.1, respectively. Supplementary files format and content: S.aureus_RNAseq_foldchange.xlsx; log2FoldChange = ≥ 1 or ≤ -1, p<0.05 Supplementary files format and content: S.aureus_RNAseq_count_data.xlsx; normalized count data
|
|
|
Submission date |
Aug 23, 2023 |
Last update date |
Aug 28, 2023 |
Contact name |
Basit Yousuf |
E-mail(s) |
byousuf@uottawa.ca
|
Phone |
6132638874
|
Organization name |
University of Ottawa
|
Street address |
2035, Othello Avenue, Ottawa
|
City |
Ottawa |
State/province |
ON |
ZIP/Postal code |
K1G3P6 |
Country |
Canada |
|
|
Platform ID |
GPL24034 |
Series (1) |
GSE241582 |
Exploring modulation in Staphylococcus aureus biofilm formation and virulence during platelet storage and its impact on platelet functionality |
|
Relations |
SRA |
SRX18848780 |
BioSample |
SAMN32395910 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|