|
| Status |
Public on Sep 14, 2021 |
| Title |
JKD6008 WT RNA-seq (no vancomycin) replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
whole bacterial cells
|
| Organism |
Staphylococcus aureus subsp. aureus str. JKD6009 |
| Characteristics |
growth media: Muller-hinton broth
antibiotic: no antibiotic
genotype: WT
sequencing type: RNA-seq
|
| Treatment protocol |
3ug/ml vancomycin for 10 mins at OD600 where indicated | 10ug/ml chloramphenicol was added to cultures with pSD-1 and derivatives
|
| Growth protocol |
Muller-Hinton media, grown at 37C to an OD600 of 3.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a GTC Phenol extraction protocol (Tollervey and Mattaj, EMBO J 1987)
Total RNA-seq libraries were constructed by NovoGene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CRISPRi_275_vs_pSD_DESeq2.xls, 2021.03.16_MUTvsWT.DEseq2_combined_output.xlsx, meta.xls pSD275v_pSDv_DESeq2.xls
|
| Data processing |
Trimming - BBTrim from BBTools
RNase III-CLASH: Merging paired reads: BBMerge from BBTools
RNase III-CLASH: Calling RNase III binding sites: pyCRAC (Webb et al Genome Biol 2014)
RNase III-CLASH: Calling RNA-RNA interactions: hyb (Travis et al Bioinformatics 2013)
dRNA-seq: Mapping, calling RNA 5' ends: ANNOgesic (Yu, Vogel, Forstner Gigascience, 2018)
Term-seq: Read mapping/alignment: bowtie2
Term-seq: 3' end mapping: bedtools genomecov
Term-seq: Statistical filtering: Custom R scripts inspired by Dar & Sorek Science 2016.
RNA-seq: Read mapping/alignment: bowtie2
RNA-seq: Statistical analysis: DESeq2 (Bioconductor)
Genome_build: NC_017341.1
Genome_build: NZ_LR027876.1
Supplementary_files_format_and_content: BEDGRAPH format, files contain mapped read depth representing RNase III-RNA interaction sites (binding sites)
Supplementary_files_format_and_content: BEDGRAPH, RNA 3' end depth (reverse complement read 5' ends)
|
| |
|
| Submission date |
Sep 30, 2020 |
| Last update date |
Jan 20, 2022 |
| 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 |
GPL29206 |
| Series (1) |
| GSE158830 |
RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance |
|
| Relations |
| BioSample |
SAMN16319604 |
| SRA |
SRX9220935 |
