|
| Status |
Public on Jan 01, 2017 |
| Title |
ΔznuA |
| Sample type |
SRA |
| |
|
| Source name |
Whole cells, ΔznuA
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
strain/background: PAO1
genotype/variation: delta-znuA
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 |
SAMN02953890 |
| SRA |
SRX671508 |
