|
| Status |
Public on Mar 26, 2024 |
| Title |
WT, 6 min, biol rep 5 (Sample 105) |
| Sample type |
SRA |
| |
|
| Source name |
SL1344
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: SL1344
genotype: WT
treatment: 6 min after rif. treatment
|
| Treatment protocol |
The cultures were treated with 500µl/ml of rifampicin (stock solution 50mg/ml resuspended in DMSO)
|
| Growth protocol |
Overnight growth from single colonies at 37 °C in LB medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol extraction followed by DNase treatment.
RNA-seq libraries were prepared by Vertis AG (Freising-Weihenstephan, Germany). The ribodepleted RNA samples were fragmented using ultrasound (4 pulses of 30 s each at 4 C). Subsequently, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/ul using a high fidelity DNA polymerase. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
proQ_htseq.csv
|
| Data processing |
Adapters were removed with Cutadapt v4.1
Alignment: STAR 2.6.0a (Dobin et al., 2013)
Quantification: htseq-count 2.0.2
Assembly: FQ312003.1, HE654724.1, HE654725.1 and HE654726.1
Supplementary files format and content: counts
Library strategy: RIF-seq
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Laura Jenniches |
| E-mail(s) |
laura.jenniches@helmholtz-hiri.de
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2/D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17070 |
| Series (2) |
| GSE234009 |
Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq] |
| GSE234010 |
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives |
|
| Relations |
| BioSample |
SAMN35571094 |
| SRA |
SRX20579232 |
