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Sample GSM7383866 Query DataSets for GSM7383866
Status Public on Jul 11, 2023
Title DNA_PTO_1
Sample type SRA
Source name SL1344
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
treatment: 15 min exposure to DNA_PTO
Treatment protocol Afterward, the bacterial solution was transferred into low-binding 5 ml tubes (LABsolute) along with the 20×PNA, peptide or PPNA solution. The final concentrations were 5 μM for all test compounds. As a negative control, cells were treated with the respective volume of sterile nuclease-free water, which was used as solvent for the test compounds. After incubating the samples for 15min at 37°C, RNAprotect Bacteria (Qiagen) was added according to the manufacturer's instructions. Following a 10-min incubation, cells were pelleted at 4°C and 21,100 ×g for 20min. The supernatant was discarded and pellets were either directly used or stored at –20°C (<1 day) for subsequent bacterial RNA isolation.
Growth protocol Bacterial overnight cultures were diluted 1:100 in fresh MHB and grown to OD600 0.5. The obtained cultures were diluted to ∼106 cfu/ml in non-cation-adjusted MHB.
Extracted molecule total RNA
Extraction protocol Total RNA was purified from bacterial pellets using the miRNeasy Mini kit (Qiagen) according to the protocol #3 described in Popella etal.(30) Briefly, cells were resuspended in 0.5 mg/ml lysozyme (Roth) in TE buffer (pH 8.0) and incubated for 5min. Afterwards, RLT buffer supplemented with β-mercaptoethanol, and ethanol were added according to the manufacturer's instructions. After sample loading, column wash-steps were performed according to the manual. RNA concentration was measured with a NanoDrop spectrophotometer.
Briefly, samples were treated with DNase (XXX) and quality was checked on a bioanalyzer (RNA chip XXX). Then, RNA was subjected to cDNA library preparation using the Corall kit (Lexogen) and including the depletion of ribosomal RNA (RiboCop-META kit, Lexogen) according to the manufacturer’s instructions. Afterwards, library samples were pooled in equimolar amounts and quality was verified using a bioanalyzer (DNA chip XXX). The cDNA pools were sequenced using the NextSeq 500 system (HighOutput flow cell, 400 M, 1x 75 cycle single-end; Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Raw RNA-Seq reads were trimmed, filtered and mapped to the SL1344 genome.
Then, BBduk was used to trim nucleobases with Phred quality scores below 10 and to remove adapter sequences.
Next, Reads were mapped against the SL1344 genome using BBMap
resulting alignments were assigned to both coding sequences and sRNAs using the featureCounts methods of the Subread package.
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 , Taxonomy ID: 216597
Supplementary files format and content: counttable.tsv: Count table in tab seperated format
Submission date May 18, 2023
Last update date Jul 11, 2023
Contact name Jakob Jeremias Jung
Organization name University of Würzburg
Department Institute of Molecular Infection Biology (IMIB)
Lab Vogel lab
Street address Josef-Schneider-Str. 2/Bau D15
City Würzburg
State/province Bayern
ZIP/Postal code 97080
Country Germany
Platform ID GPL21220
Series (1)
GSE232819 A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics
BioSample SAMN35159970
SRA SRX20431366

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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