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Status |
Public on Mar 26, 2024 |
Title |
WT, 4 min, biol rep 1 (Sample 15) |
Sample type |
SRA |
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|
Source name |
SL1344
|
Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
Characteristics |
strain: SL1344 genotype: WT treatment: 4 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).
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
cspCE_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
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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 |
SAMN35571184 |
SRA |
SRX20579134 |