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Sample GSM4569746 Query DataSets for GSM4569746
Status Public on Dec 21, 2020
Title PAO1_rpmi_2
Sample type SRA
 
Source name Pseudomonas aeruginosa mid-log culture
Organism Pseudomonas aeruginosa PAO1
Characteristics treatment: untreated
media: RPMI-1640 + 5% MHB
growth phase: mid-log
Treatment protocol P. aeruginosa was grown in each medium to OD600 0.5, cultures were split into two equal volumes and effective concentrations of AZM were added to one of the two aliquots (samples denoted as AZM treated). To AZM cultures, AZM was added at an effective concentration to decrease growth without total inhibition (MHB: 16 ug/mL; RPMI: 8 ug/mL; serum: 6 ug/mL)
Growth protocol P. aeruginosa was inoculated into 25 mL of each growth medium at a startingOD of 0.05 and grown to mid log
Extracted molecule total RNA
Extraction protocol Sixty minutes post-treatment, bacterial cells were collected and mixed 1:2 volume wise with RNA protect Bacteria Reagent (QIAGEN). RNA was extracted using RNeasy mini kit (QIAGEN).
RNA was quantified using a Nanodrop-1000 (ThermoFisher). RNA quality and quantity were assessed on an Agilent Bioanalyzer. rRNA was depleted (Ribo-Zero depletion kit, Illumina), and cDNA libraries were prepared using the KAPA RNA HyperPrep Kit (KAPA Biosystems) and sequenced through the University of British Columbia Sequencing Consortium (Illumina HiSeq-2500)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description rpmi2
Data processing Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PAO1 reference genome using STAR v2.6.1a read count tables were generated from bam files using htseq-count v.2.5
Significance and fold changes calculated in R (3.6.2) using DEseq2 package with Likelihood Ratio Test
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample
 
Submission date May 27, 2020
Last update date Dec 21, 2020
Contact name Amy H. Lee
Organization name Simon Fraser University
Department Molecular Biology and Biochemistry
Lab Amy Lee
Street address 8888 University Drive
City Burnaby
State/province BC
ZIP/Postal code V5A1S6
Country Canada
 
Platform ID GPL18782
Series (1)
GSE151259 Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media
Relations
BioSample SAMN15031774
SRA SRX8405315

Supplementary file Size Download File type/resource
GSM4569746_rpmi_2.count.txt.gz 22.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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