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Sample GSM8045613 Query DataSets for GSM8045613
Status Public on Mar 17, 2024
Title control_30mins_2
Sample type SRA
 
Source name whole cell
Organism Staphylococcus aureus subsp. aureus str. JKD6008
Characteristics tissue: whole cell
cell line: strain JKD6008 (vancomycin intermediate, VISA)
genotype: VISA
treatment: no treatment
Treatment protocol Where applicable, cultures were treated with 8ug/ml of vancomycin for 30mins and then harvested into GTC-phenol buffer.
Growth protocol S. aureus str. JKD6008 was grown in Muller-Hinton media to an OD600 of 0.8 before treatment
Extracted molecule total RNA
Extraction protocol GTF-phenol (Tollervey & Mattaj EMBO J 1987; PMID: 2953599)
Libraries prepared by Novagene using prokaryotic directional mRNA library preparation (with rRNA removal).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing prepocessing using BBDuk. BBDuk was used to trim the 5’ adapter sequence of the raw data using the parameters ‘ktrim=l k=23 mink=11 hdist=1’ followed by quality trimming with the parameters ‘qtrim=rl trimq=30’(Bushnell, 2014). After trimming, BBmerge was used to merge the paired-end reads using the default parameters (Bushnell et al, 2017)
mapped using BBMap
Read counts for each feature was computed using bedtools coverage (https://bedtools.readthedocs.io/en/latest/)(PMID: 25199790)
Differential gene expression analysis was performed using DESeq2 (Love et al, 2014)(PMID: 25516281)
Assembly: GCF_000145595.1
Supplementary files format and content: gene count table (raw reads counts)
Supplementary files format and content: Deseq2 output table of differentially expressed genes
 
Submission date Jan 30, 2024
Last update date Mar 17, 2024
Contact name Jai Justin Tree
E-mail(s) j.tree@unsw.edu.au
Phone +61 2 938 59142
Organization name University of New South Wales
Department School of Biotechnology and Biomolecular Sciences
Lab Tree lab
Street address Rm s110 Bldg F25, UNSW, Gate 11 Botany St
City Sydney
State/province NSW
ZIP/Postal code 2033
Country Australia
 
Platform ID GPL31256
Series (2)
GSE254530 The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus [RNA-seq]
GSE254533 The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus.
Relations
BioSample SAMN39667165
SRA SRX23443812

Supplementary file Size Download File type/resource
GSM8045613_Cont2_30mins_RNA.txt.gz 11.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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