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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.
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|
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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)
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|
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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 |