|
| Status |
Public on Sep 08, 2022 |
| Title |
SG511-02REV-03 [QOBWO030A6] |
| Sample type |
SRA |
| |
|
| Source name |
lab grown bacteria
|
| Organism |
Staphylococcus aureus |
| Characteristics |
treatment1: untreated
genotype/phenotype: Cervimycin resistent 2, suppressor mutant
strain: SG511
|
| Treatment protocol |
20 mL culture were harvested (5 min, 8,000 x 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.
|
| Growth protocol |
S. aureus cultures were grown in TSB at 37 °C with shaking until an OD600 of 1.0 was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Monarch™ Total RNA Miniprep Kit (New England Biolabs) following the manufacturer’s instructions and stored at −80 °C. Quality and quantity of total RNA were determined by agarose gel electrophoresis.
Per replicate, a total amount of 400 ng RNA was subjected to rRNA depletion. For rRNA depletion and cDNA library construction the IlluminaTM Stranded Total RNA Prep Ligation with Ribo Zero Plus Kit was used according to the manufacturer’s instructions. Libraries were sequenced as single-read (101 bp read length) on a NovaSeq 6000 platform (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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: NZ_CP076660.1
Supplementary files format and content: counts.txt: A tab separated matrix with samples as columns and genes as rows
|
| |
|
| Submission date |
Jun 16, 2022 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Kay Nieselt |
| E-mail(s) |
[email protected]
|
| Phone |
(+49) 70712978981
|
| Organization name |
Institute for Bioinformatics and Medical Informatics
|
| Department |
Department for Computer Science
|
| Lab |
Integrative Transcriptomics
|
| Street address |
Sand 14
|
| City |
Tübingen |
| State/province |
DE |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27158 |
| Series (1) |
| GSE206309 |
Cervimycin resistant Staphylococcus aureus strains display a vancomycin intermediate resistant phenotype |
|
| Relations |
| BioSample |
SAMN29152244 |
| SRA |
SRX15746458 |
