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Sample GSM4232896 Query DataSets for GSM4232896
Status Public on Feb 18, 2020
Title Control_3
Sample type SRA
 
Source name bacterial culture (LBN media)
Organism Pseudomonas aeruginosa PAO1
Characteristics media additive(s): N/A
Growth protocol Bacteria were grown aerobically overnight in LB at 37oC. The next day, bacteria were diluted 100-fold into 20 ml of fresh LBN 6.5 then aliquoted into 4 tubes containing 5 ml each. Tubes were incubated anaerobically at 37oC under static conditions for 3 hr. Final concentrations of 1 mM EDTA and/or 15 mM NaNO2 were added to each tube. Then, cells were incubated for an additional 2.5 hr.
Extracted molecule total RNA
Extraction protocol Qiagen Bacteria Protect Rneasy Mini kit, Epicentre Ribo-Zero rRNA removal kit
mRNA reverse transcribed using Illumina TruSeq stranded mRNA library preparation kit. Libraries barcoded with 8bp oligos then amplified for 15 cycles
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description ribosomally depleted RNA
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 PA14 genome using STARv2.5.2b
read count tables were generated using htseq-count v.2.5
Genome_build: PAO1 NC_002516 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample
 
Submission date Dec 26, 2019
Last update date Feb 18, 2020
Contact name Erin Gill
E-mail(s) [email protected]
Organization name University of British Columbia
Street address 2259 Lower Mall
City Vancouver
State/province British Columbia
ZIP/Postal code V6T 1Z4
Country Canada
 
Platform ID GPL18782
Series (1)
GSE142611 AB569, A Nontoxic Chemical Tandem That Kills Major Human Pathogenic Bacteria
Relations
BioSample SAMN13683002
SRA SRX7442753

Supplementary file Size Download File type/resource
GSM4232896_L3.count.txt.gz 21.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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