|
| Status |
Public on Mar 17, 2024 |
| Title |
control_30mins_3 |
| 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 |
SAMN39667164 |
| SRA |
SRX23443813 |
