GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7731258

Query DataSets for GSM7731258

Status

Public on Aug 28, 2023

Title

BAC317-TSB1b

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