|
| Status |
Public on Dec 10, 2013 |
| Title |
sphR mutant in pyruvate, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas aeruginosa sphR mutant in MOPS pyruvate
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
genotype: PAO1 sphR deletion
treatment: pyruvate control
|
| Treatment protocol |
Cell suspension was treated with two volumes of RNA Protect Bacterial Reagent (Qiagen) and processed to a wet pellet as per manufacturer's instructions
|
| Growth protocol |
Cells were pregrown for 18 h in MOPS with 25 mM pyruvate and 5 mM glucose and then resuspended in MOPS pyruvate or MOPS pyruvate + 1:50 dilution of Survanta
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from RNA Protect-treated pellets using the Qiagen RNeasy kit using lysozyme-aided lysis. RNA from the first round of columns was treated with DNase I and another round of RNeasy conducted including the on-column DNase step.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA was prepared from 50 ng of whole RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 2.4 ug of cRNA were hybridized on the Pseudomonas aeruginosa PAO1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 7G Scanner.
|
| Data processing |
Probe intensities were first generated using the AGCC program (Affymetrix). Probe-level intensities were background-corrected, normalized, and summarized, and Robust Multichip Average (RMA) statistics were calculated for each probe set and sample as is implemented in Partek Genomic Suites®, version 6.6
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
Dec 10, 2013 |
| Contact name |
Matthew J Wargo |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Vermont
|
| Department |
Department of Microbiology and Molecular Genetics
|
| Street address |
95 Carrigan Dr
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE48982 |
Pseudomonas aeruginosa response to lung surfactant |
|
