|
| Status |
Public on Sep 20, 2011 |
| Title |
PA14-mexR QSM C30 2hr 37C planktonic cell |
| Sample type |
RNA |
| |
|
| Source name |
Channel 1
|
| Organism |
Pseudomonas aeruginosa PA14 |
| Characteristics |
cell type: planctonic cells
strain: PA14_mexR
medium: QSM minimal medium
compound: 50 µM C30
time: 2 hr
temp: 37 ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Overnight culture in LB+Tc75 was washed with 1 volume of QSM medium (OS minimal medium + 0.1% Adenosine as carbon source) twice, and re-inoculated into 200 ml QSM medium in 1 L flask start with OD600= 0.02. The culture was incubated at 37 ºC with shaking at 250 rpm. When culture grows to mid-exponential phase (OD600=0.25), C30 was added to a final concentration of 50 µM and the culture was incubated for additional 2 hr. Cells were harvested, total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).
|
| Label |
biotin
|
| Label protocol |
Following affymetrix protocol.cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
|
| |
|
| Hybridization protocol |
Following affymetrix protocol.cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
|
| Scan protocol |
Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).”
|
| Description |
RNA extracted from planktonic cells of PA14_mexR after 2 hr growth after adding 50 µM C30 in QSM minimal medium when OD600 reaches 0.25.
|
| Data processing |
MAS 5.0 Expression Analysis Default Setting
|
| |
|
| Submission date |
Sep 21, 2010 |
| Last update date |
Sep 20, 2011 |
| Contact name |
Mingming Pu |
| E-mail(s) |
pu.mingming@gmail.com
|
| Organization name |
Texas A&M University
|
| Department |
Chemical Engineering
|
| Lab |
Thomas K. Wood
|
| Street address |
3122 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE24262 |
PA14_mexR vs. wildtype planktonic cells in minimal medium with C-30 |
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