|
| Status |
Public on May 19, 2015 |
| Title |
Escherichia coli wild type vs luxS mutants without H2O2 Rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type, without H2O2
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K-12 W3110
treatment: none
genotype: wild type
|
| Treatment protocol |
three different concentrations, without H2O2, 10% (v/v) or 30% H2O2 were added directly to the cell cultures of wild type or luxS mutants, OD of which is 1.0. Treated samples were continuously incubated at 30 degree Celcius for 30min
|
| Growth protocol |
Overnight culture of E. coli in LB was diluted in LB supplemented with 0.8% glucose to OD600=0.02 and was continuously incubated at 30 degree celcius with shaking until its OD600 reached 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 5ml cell culture after 30min incubation with or without H2O2 treatment using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol
|
| Label |
Cy5
|
| Label protocol |
Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets
|
| |
|
| Channel 2 |
| Source name |
luxS mutants, without H2O2
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K-12 W3110
treatment: none
genotype: luxS
|
| Treatment protocol |
three different concentrations, without H2O2, 10% (v/v) or 30% H2O2 were added directly to the cell cultures of wild type or luxS mutants, OD of which is 1.0. Treated samples were continuously incubated at 30 degree Celcius for 30min
|
| Growth protocol |
Overnight culture of E. coli in LB was diluted in LB supplemented with 0.8% glucose to OD600=0.02 and was continuously incubated at 30 degree celcius with shaking until its OD600 reached 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 5ml cell culture after 30min incubation with or without H2O2 treatment using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol
|
| Label |
Cy3
|
| Label protocol |
Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets
|
| |
|
| |
| Hybridization protocol |
Standard Agilent procedures
|
| Scan protocol |
Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1
|
| Description |
Biological replicate 1 of 2
|
| Data processing |
Agilent Feature Extraction Software v. 9.5.3.1 was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
May 23, 2012 |
| Last update date |
May 19, 2015 |
| Contact name |
Aram Kang |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Chemical and Biomedical Engineering
|
| Lab |
Chang Lab
|
| Street address |
62 Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637459 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL13360 |
| Series (1) |
| GSE38186 |
Escherichia coli K-12: 0%, 10% and 30% hydrogen peroxide (H2O2) treatments, in wild type and luxS mutants |
|
