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Sample GSM7440490 Query DataSets for GSM7440490
Status Public on Mar 26, 2024
Title ΔcspCE, 0 min, biol rep 1 (Sample 18)
Sample type SRA
Source name SL1344
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
genotype: {delta}cspCE
treatment: 0 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 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
Submission date Jun 02, 2023
Last update date Mar 26, 2024
Contact name Laura Jenniches
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
BioSample SAMN35571181
SRA SRX20579137

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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