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Sample GSM1466898 Query DataSets for GSM1466898
Status Public on Jan 01, 2017
Title PAO1
Sample type SRA
 
Source name Whole cells, WT
Organism Pseudomonas aeruginosa PAO1
Characteristics strain/background: PAO1
genotype/variation: WT
cell type: whole cells
Treatment protocol All samples were grown in cation-defined media.
Growth protocol Wild-type PAO1 and the ΔznuA deletion mutant were inoculated at OD600=0.05 from an overnight culture, and grown aerobically to OD600=0.6 in cation-defined media. Three biological replicates were grown on separate days for each strain.
Extracted molecule total RNA
Extraction protocol Cells were collected and lysed using TRIzol/Chloroform. Subsequent RNA extraction was performed using an Ambion PureLink RNA Isolation kit. RNA was treated with DNase I (Roche) and cleanup on a Ambion PureLink RNA isolation column. Ribosomal RNA was removed using RiboZero Bacterial (Gram-) depletion kit (Illumina). The RNA integrity was assessed on a BioAnalyzer (RIN > 9). Biological replicates were pooled.
Illumina TruSeq Stranded Total RNA LT Sample Prep Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Ribosomal RNA removed.
Data processing Alignment (BOWTIE2).
Counts and direct comparison between samples (DESeq).
Genome_build: NC_002516.2
Supplementary_files_format_and_content: CountsRNA6.txt, CountsRNA7.txt: Text files with counts/sample.
Supplementary_files_format_and_content: PseudomonasDESeq.txt: Text file with relative counts between ΔznuA and PAO1.
 
Submission date Aug 06, 2014
Last update date May 15, 2019
Contact name Bart Eijkelkamp
E-mail(s) [email protected]
Organization name University of Adelaide
Street address North Tce
City Adelaide
State/province SA
ZIP/Postal code 5000
Country Australia
 
Platform ID GPL18782
Series (1)
GSE60177 Zinc acquisition in Pseudomonas aeruginosa
Relations
BioSample SAMN02953889
SRA SRX671507

Supplementary file Size Download File type/resource
GSM1466898_CountsRNA6.txt.gz 379.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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