|
| Status |
Public on Feb 15, 2014 |
| Title |
no substrate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Cells harvested at 30 min post induction
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
sub-strain: PAO1-UW
genotype: wild-type
|
| Treatment protocol |
At 30 min post induction with 2-oxoglutarate, 0.5 mL of culture was treated with 1.0 mL of RNAprotect Bacterial reagent (Qiagen).
|
| Growth protocol |
P. aeruginosa PAO1 was grown in 1 mL of nutrient broth (Oxoid number 2) at 37 C, 200 rpm, until an OD 600 of 0.3 was reached. Cells were induced with either 0 or 20 mM 2-oxoglutarate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the enzymatic lysis and proteinase K digestion method of Qiagen Rneasy with on-column DNA digestion.
|
| Label |
biotin
|
| Label protocol |
Samples were processed according to the Prokaryotic Target Preparation Protocol in Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 10 ug of RNA was used to synthesize cDNA via random primers and SuperScript II reverse transcriptase. cDNA was purified using Qiagen MinElute PCR purification columns. The resulting cDNA was fragmented and labeled with biotin.
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 50C 60 rpm on GeneChip P. aeruginosa Genome Array with rotation at 60 rpm. GeneChips were processed with an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 P. aeruginosa array protocol (as specified in the Affymetrix GeneChip Expression Analysis Technical Manual), using stains from the Affymetrix Hybridization, Wash, and Stain Kit.
|
| Scan protocol |
Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus
|
| Description |
Gene expression from cells grown in rich media and induced with no substrate
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
|
| |
|
| Submission date |
Jan 13, 2014 |
| Last update date |
Feb 15, 2014 |
| Contact name |
Christopher Nomura |
| E-mail(s) |
[email protected]
|
| Phone |
315-470-6854
|
| Organization name |
SUNY-ESF
|
| Department |
Chemistry
|
| Lab |
336 Jahn
|
| Street address |
1 Forestry Dr.
|
| City |
Syracuse |
| State/province |
NY |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE54032 |
Transcriptional response to 2-oxoglutarate (alpha-ketoglutarate) in Pseduomonas aeruginosa PAO1 |
|
