|
| Status |
Public on Apr 06, 2005 |
| Title |
Aerobic GSNO Chemostat Run 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes
|
| Organism |
Escherichia coli |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source name |
Steady-state continuous cultured control samples in absence of GSNO
|
| Organism |
Escherichia coli |
| Extracted molecule |
total RNA |
| |
|
| |
| Description |
Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 54 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode and automated adjustment of stirring rate. Cells were grown as above to steady-state, At steady-state, GSNO was added to the chemostat culture and to the nutrient feed at a final concentration of 200 uM unless otherwise stated. Samples were taken immediately prior to the addition of GSNO and after a period of 5 min exposure to GSNO for subsequent analysis using microarrays. Cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
|
| |
|
| Submission date |
Dec 21, 2004 |
| Last update date |
Oct 28, 2005 |
| Contact name |
Jason Barrett |
| E-mail(s) |
J.A.Barrett@sheffield.ac.uk
|
| Phone |
(+44) 114 2222834
|
| Organization name |
University of Sheffield
|
| Department |
Department of Molecular Biology and Biotechnology
|
| Street address |
Firth Court, Western Bank
|
| City |
Sheffield |
| State/province |
South Yorkshire |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL534 |
| Series (1) |
| GSE2095 |
Transcriptional responses of Escherichia coli to GSNO under defined chemostat conditions. |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Cy3:Cy5 ratio following background correction, log2 transformation, Loess normalisation |
| CH1_MEAN |
Mean data in Cy3 Channel |
| CH1_BKD_MEAN |
Background Mean in Cy3 Channel |
| CH1_AREA |
Spot Area in Cy3 Channel |
| CH1_BKD_AREA |
Background Area in Cy3 Channel |
| CH1_RAW |
Raw signal output data obtained from image analysis algorithm in Cy3 Channel |
| CH1_BKD_RAW |
Raw background output data obtained from image analysis algorithm in Cy3 Channel |
| CH1_SD |
Standard Deviation obtained in Cy3 Channel |
| CH1_BKD_SD |
Background Standard Deviation in Cy3 Channel |
| CH2_MEAN |
Mean data in Cy5 Channel |
| CH2_BKD_MEAN |
Background Mean in Cy5 Channel |
| CH2_AREA |
Spot Area in Cy5 Channel |
| CH2_BKD_AREA |
Background Area in Cy5 Channel |
| CH2_RAW |
Raw signal output data obtained from image analysis algorithm in Cy5 Channel |
| CH2_BKD_RAW |
Raw background output data obtained from image analysis algorithm in Cy5 Channel |
| CH2_SD |
Standard Deviation obtained in Cy5 Channel |
| CH2_BKD_SD |
Background Standard Deviation in Cy5 Channel |
