|
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 |