|
| Status |
Public on Mar 17, 2024 |
| Title |
JKD6008_untagged_bkg_3 |
| Sample type |
SRA |
| |
|
| Source name |
strain JKD6008 (vancomycin intermediate, VISA)
|
| Organism |
Staphylococcus aureus subsp. aureus str. JKD6008 |
| Characteristics |
cell line: strain JKD6008 (vancomycin intermediate, VISA)
genotype: VISA
treatment: untagged_background_control_3
|
| 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 |
other |
| Extraction protocol |
as per CLASH protocol (PMID: 37925184)
Libraries were prepared using RNase III-CLASH (PMID: 37925184). This technique captures RNA-RNA interactions associated with RNase III
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Not included in the final processed data
|
| Data processing |
library strategy: RNase III-CLASH
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).
BBmerge was used to merge the paired-end reads using the default parameters (Bushnell et al, 2017)
RNase III-RNA and RNA-RNA interactions were determined using the pipeline Hyb-CRAC-R avaiable at https://github.com/IgnatiusPang/Hyb-CRAC-R
Assembly: GCF_000145595.1 with additional custom annotations of 5'UTRs and 3'UTRs from PMID: 35732665
Supplementary files format and content: Final_RATT_VISACLASH.txt, RNA-RNA interactions recovered from RNase III_CLASH. Format as per https://github.com/IgnatiusPang/Hyb-CRAC-R
Supplementary files format and content: Sa_JKD6008_annot_updated.gtf; updated annotation file in GTF format
|
| |
|
| 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 |
GPL34143 |
| Series (2) |
| GSE254532 |
The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus [RNase III-CLASH] |
| GSE254533 |
The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureus. |
|
| Relations |
| BioSample |
SAMN39667406 |
| SRA |
SRX23444034 |
