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| Status |
Public on Apr 02, 2024 |
| Title |
S. aureus 1 M NaCl biol rep 3 |
| Sample type |
SRA |
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| Source name |
Staphylococcus aureus SG511 Berlin
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| Organism |
Staphylococcus aureus |
| Characteristics |
cell type: bacterial cells
cell line: Staphylococcus aureus SG511 Berlin
growth phase: exponential growth phase
treatment: grown in the presence of 1 M NaCl
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| Treatment protocol |
Cultures of S. aureus SG511 were grown in TSB containing 1 M NaCl at 37 °C with aeration until an OD600 of 1.0 was reached.
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| Growth protocol |
Cultures of S. aureus SG511 were grown in TSB at 37 °C with aeration until an OD600 of 1.0 was reached.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction, 1 mL culture was harvested (5 min, 8,000 ´ g, RT), the cells were resuspended in 1 mL RNA protect buffer (New England Biolabs, Frankfurt am Main, Germany) and incubated for 5 min at RT. The cells were resuspended in 200 µL TE buffer with 25 µg lysostaphin and cell lysis was achieved by incubation at 37 °C for 30 min. RNA was extracted using the Monarch™ Total RNA Miniprep Kit (New England Biolabs) following the manufacturer’s instructions and stored at −80 °C, before submission to the Genewiz sequencing facility (Leipzig, Germany). RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria).
RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
QOBWO021A7
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| Data processing |
Alignment: HISAT2, version , parameters --no-spliced-alignment --rna-strandness R
Counting: featureCounts, version 1.6.4, parameters -s 2 -t transcript -g locus_tag
Assembly: NCBI Reference Sequence: NZ_CP076660.1
Supplementary files format and content: tab-delimited text file including the normalized hit counts for each Sample, the calculated Log2 fold change and the p-values
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| Submission date |
Dec 19, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Alina Hoffmann |
| E-mail(s) |
[email protected]
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| Organization name |
University Hospital Bonn
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| Street address |
Venusberg Campus 1
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| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
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| Platform ID |
GPL27158 |
| Series (2) |
| GSE250540 |
The unusual mode of action of the polyketide glycoside antibiotic cervimycin C [II] |
| GSE250541 |
The unusual mode of action of the polyketide glycoside antibiotic cervimycin C |
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| Relations |
| BioSample |
SAMN38931845 |
| SRA |
SRX22969564 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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