|
| Status |
Public on Mar 17, 2007 |
| Title |
WT_tp4_hyb2: 869 min post-inoculation |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
E. coli wild-type tp4: 869 min post-inoculation
|
| Organism |
Escherichia coli |
| Characteristics |
Escherichia coli MG1655
wild-type
869 min post-inoculation
A600 = 038
|
| Growth protocol |
E. coli MG1655 wild-type and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 degrees C and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow. Growth was monitored as absorbance at 600nm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells that had been diluted into ice-cold RNA-Later (Ambion) immediately upon culture sampling and purified using RN-Easy columns with DNase treatment (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
RNA was labeled by first-strand cDNA synthesis using reverse transcriptase, random primers, and aminoallyl-dUTP incorporation; Cy-3 or Cy-5 dyes were chemically coupled in vitro to the aminoallyl-derivatized cDNA
|
| |
|
| Channel 2 |
| Source name |
E. coli wild-type tp1: 780 min post-inoculation
|
| Organism |
Escherichia coli |
| Characteristics |
Escherichia coli MG1655
wild-type
780 min post-inoculation
A600 = 0.143
|
| Growth protocol |
E. coli MG1655 wild-type and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 degrees C and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow. Growth was monitored as absorbance at 600nm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells that had been diluted into ice-cold RNA-Later (Ambion) immediately upon culture sampling and purified using RN-Easy columns with DNase treatment (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
RNA was labeled by first-strand cDNA synthesis using reverse transcriptase, random primers, and aminoallyl-dUTP incorporation; Cy-3 or Cy-5 dyes were chemically coupled in vitro to the aminoallyl-derivatized cDNA
|
| |
|
| |
| Hybridization protocol |
Equal amounts of the Cy-3- and Cy-5-labeled samples were hybridized in triplicate to microarrays by using a Discovery system and ChipMap reagents (Ventana Medical Systems). For all microarrays, the experimental sample was labeled with Cy-5, and the control, from early logarithmic growth of E. coli MG1655 wild type on minimal glucose medium, was labeled with Cy-3.
|
| Scan protocol |
For all microarrays, the experimental sample was labeled with Cy-5, and the control, from early logarithmic growth of E. coli MG1655 wild type on minimal glucose medium, was labeled with Cy-3. Hybridized slides were scanned on a GenePix 4000 scanner (Axon Instruments), and the data were collected by using GENEPIX 5.0 software.
|
| Description |
WT_tp4_hyb2
|
| Data processing |
The data were normalized by using a local Loess algorithm
|
| |
|
| Submission date |
Mar 14, 2007 |
| Last update date |
Sep 09, 2008 |
| Contact name |
Joe Grissom |
| E-mail(s) |
jgrissom@ou.edu
|
| Phone |
405-325-4906
|
| URL |
http://www.ou.edu/microarray/
|
| Organization name |
University of Oklahoma
|
| Department |
Advanced Center for Genome Technology
|
| Lab |
Conway Lab
|
| Street address |
101 David L. Boren Blvd
|
| City |
Norman |
| State/province |
OK |
| ZIP/Postal code |
73019 |
| Country |
USA |
| |
|
| Platform ID |
GPL4995 |
| Series (1) |
| GSE7265 |
Time series analysis of glucose-lactose diauxie: involvement of stringent response |
|
