|
| Status |
Public on Feb 20, 2024 |
| Title |
JKD6009 ∆vigR pRAB11::MS2 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole cell lysate
|
| Organism |
Staphylococcus aureus |
| Characteristics |
tissue: whole cell lysate
cell line: JKD6009
cell type: bacterial cell
genotype: deltavigR3'UTR pRAB11::MS2
|
| Treatment protocol |
Test and control strains have an MS2-vigR3'UTR fusion or MS2 alone, respectively.
|
| Growth protocol |
Strains were grown in BHI media supplemented with 15 ug/mL chloramphenicol at 37C with 180 rpm shaking to an OD600nm 3.0. Constructs were then induced with 0.4 uM ATc and grown for a further 15 min at 37oC with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As per MAPS protocol (PMID: 25891076)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RNA was prepared from samples using the MAPS protcol (PMID: 25891076)
|
| Data processing |
FASTQ files were mapped and reads depth counted using the CRAC_pipeline_PE.py available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines
From the CRAC_pipeline_PE output, the mapped reads in GTF format that have neeb collapsed into blocks and reads with mutations removed ("blocks_nomuts") were converted to BED format using pyGTF2bed.py int eh pyCRAC suite (Webb et al., 2014; PMID: 24393166).
BED formatted files were used as input for the peak calling software BLOCKBUSTER (PMID: 19584066; https://www.bioinf.uni-leipzig.de/~david/LIFE/LIFE/blockbuster.html)
Peak height was calculated using HTSeq (PMID: 25260700)
Statistically signficant peaks (sites enriched in the test condition relative to controls) was determined using DESeq2 (PMID: 25516281)
Assembly: GCF_900607245.1
Supplementary files format and content: BED format fies, read depth in graph format for each sample. These files are the output of CRAC_pipeline_PE and pyGTF2bed. They are input for peak calling with blockbuster, HTSeq, and DESeq2
Supplementary files format and content: final_peaks.csv. This file contains the output from DEseq2. The table is all peaks that have an adjusted p-value of <0.1 and an increase in signal in the test condition. Each peak is labelled with a unique idnetifier in column 1 starting with "clip_peak"
Supplementary files format and content: final_peaks_overlap_features.gff. Peaks that are signficantly enriched in the test condition (from final_peaks.csv) were intersected with genomic features in GFF file for GCF_900607245.1. The output GFF file can be referenced against the DESeq2 DE expression data using the unique peak idnentifier "clip_peak_" in column 9.
|
| |
|
| Submission date |
Jan 10, 2024 |
| Last update date |
Feb 20, 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 |
GPL30817 |
| Series (1) |
| GSE252940 |
The 3’ UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions |
|
| Relations |
| BioSample |
SAMN39336602 |
| SRA |
SRX23154402 |
