|
| Status |
Public on Dec 21, 2018 |
| Title |
pilR deletion mutant, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
P. aeruginosa ΔpilR cells
|
| Organism |
Pseudomonas aeruginosa PAK |
| Characteristics |
strain: PAK
genotype: deletion of pilR (PA4547)
|
| Growth protocol |
All cells were grown on Lennox Broth (LB) plates with 1.5% agar, for 16h at 37 degrees C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from a half petri dish worth of cells was extracted using the RNeasy mini kit (Qiagen) with both on column and in solution DNase digestion
rRNA was depleted using a ribo-zero rRNA depletion kit. RNA libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired end reads were concatenated in Rockhopper
Reads were aligned to the PAO1 reference genome
Raw fastq files from Illumina were used as input for Rockhopper analyses. Default parameters were used, with reverse complementation of reads
Raw transcript levels, normalized transcript levels, RPKM transcript levels, and expression transcript levels (transcript levels normalized by the upper quartile of gene expression) were obtained using Rockhopper software (McClure et al., 2013)
|
| |
|
| Submission date |
Apr 02, 2018 |
| Last update date |
Dec 21, 2018 |
| Contact name |
Sara LN Kilmury |
| E-mail(s) |
[email protected]
|
| Organization name |
McMaster University
|
| Department |
Biochemistry
|
| Lab |
Dr. Lori Burrows
|
| Street address |
1280 Main St. W Room 4H13
|
| City |
Hamilton |
| State/province |
ON |
| ZIP/Postal code |
L8S 4L8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24806 |
| Series (1) |
| GSE112597 |
The Pseudomonas aeruginosa PilSR two-component system regulates both twitching and swimming motilities |
|
| Relations |
| BioSample |
SAMN08832574 |
| SRA |
SRX3873097 |
