|
| Status |
Public on Apr 06, 2005 |
| Title |
Anaerobic GSNO Chemostat Run 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Steady-state continuous cultured control samples in absence of GSNO
|
| Organism |
Escherichia coli |
| Extracted molecule |
total RNA |
| |
|
| Channel 2 |
| Source name |
Steady-state continuous cultured experiment samples in presence of 200uM GSNO for 5 minutes
|
| 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. In order to establish anaerobic growth, nitrogen was sparged through the chemostat medium prior to inoculation and throughout the course of the experiment at a rate of 0.2 l/min. No dissolved oxygen was detectable using the OxyProbe. Sodium fumarate was added to anaerobic medium at a final concentration of 50 mM to act as a terminal electron acceptor. 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 |
Jan 06, 2005 |
| 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) |
| GSE2129 |
Transcriptional responses of Anaerobically grown 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 |
