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Sample GSM5556740 Query DataSets for GSM5556740
Status Public on Sep 03, 2024
Title RiboSeq_EV1
Sample type SRA
 
Source name Ribo-seq of planktonic culture of Pseudomonas aeruginosa PA01 treated with 0.2% arabinose from 45 min after inoculation (OD of 0.05) to OD 0.5-0.7
Organism Pseudomonas aeruginosa PAO1
Characteristics cell line: pHERD20T
strain: PA01
Treatment protocol Expression of pHERD20T based plasmids was induced with 0.2 % arabinose after 45 min of growth. Cells were harvested between OD600 of 0.5 - 0.7.
Growth protocol Bacterial cultures were grown in liquid LB supplemented with 400 µg/ml carbenicillin at 37 °C and 180 rpm. Cultures were inoculated with OD600 of 0.05.
Extracted molecule total RNA
Extraction protocol For the isolation of ribosome protected RNA, bacterial cells were harvested by fast filtration and flash frozen in liquid nitrogen. Cell lysates were subjected to MNase digestion and subsequently separated into their different components by rate zonal centrifugation on a sucrose gradient. The fraction containing 70S ribosomes was collected and ribosome protected RNA was isolated with the Direct-zol™ Kit (Zymo Research). RNA fragments between 26 – 34 nt were extracted from denaturing 15% polyacrylamide gels and subjected to cDNA library preparation using the NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs) following manufacturer´s instructions.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description ribosome protected RNA
Data processing Library strategy: Ribo-Seq
RiboSeq
clipping using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
bowtie -m 1
RNASeq
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie --trim3 1 -m 1
RNASeq_repetition
cutadapt --nextseq-trim=20 -g 'TTTTT;min_overlap=1' -G 'GGGGGGG;min_overlap=3' -m 36
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie2 --very-sensitive-local -I 100 -X 1200
Genome_build: Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
Supplementary_files_format_and_content: contains RiboSeq_EV[1-2], RiboSeq_PleD[1-2], RNASeq_EV[1-2], and RNASeq_PleD[1-2] data
Supplementary_files_format_and_content: contains RNASeq repetition samples
Supplementary_files_format_and_content: raw count data
 
Submission date Sep 03, 2021
Last update date Sep 03, 2024
Contact name Matthias Preusse
Organization name Helmholtz Centre for Infection Research
Street address Inhoffenstr. 7
City Braunschweig
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL18782
Series (1)
GSE183394 Pseudomonas aeruginosa post-translational responses to elevated c-di-GMP levels
Relations
BioSample SAMN21216050
SRA SRX12008579

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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