|
| 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 |
