|
| Status |
Public on Mar 06, 2009 |
| Title |
SmUA159-pH5.5-rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pH 5.5
|
| Organism |
Streptococcus mutans |
| Characteristics |
strain: UA159
|
| Treatment protocol |
The cells were grown at either pH 5.5 or pH 7.5 for additional 2 hours.
|
| Growth protocol |
Streptococcus mutans UA159 was grown in a TYG broth (3% tryptone, 0.3% yeast extract and 20 mM glucose) up to a density of 0.6 at OD600.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from S. mutans UA159 cells by a FastPrep method using 1 ml of cool Trizol (Invitrogen). The RNAs were treated with RNase-free DNase 1 and purified by Qiagen RNeasy mini columns
|
| Label |
AlexaFluor 647
|
| Label protocol |
The purified RNAs were used to generate cDNA probes by an indirect labeling method based on the protocol from TIGR. The cDNAs were coupled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
pH 7.5
|
| Organism |
Streptococcus mutans |
| Characteristics |
strain: UA159
|
| Treatment protocol |
The cells were grown at either pH 5.5 or pH 7.5 for additional 2 hours.
|
| Growth protocol |
Streptococcus mutans UA159 was grown in a TYG broth (3% tryptone, 0.3% yeast extract and 20 mM glucose) up to a density of 0.6 at OD600.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from S. mutans UA159 cells by a FastPrep method using 1 ml of cool Trizol (Invitrogen). The RNAs were treated with RNase-free DNase 1 and purified by Qiagen RNeasy mini columns
|
| Label |
AlexaFluor 555
|
| Label protocol |
The purified RNAs were used to generate cDNA probes by an indirect labeling method based on the protocol from TIGR. The cDNAs were coupled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
The labeled cDNA probes were hybridized to the S. mutans UA159 microarray slides obtained from PFGRC (http://pfgrc.tigr.org). Array hybridization was conducted using a protocol from the PFGRC with minor modification.
|
| Scan protocol |
After hybridization, washes and dried, the array slides were scanned by ScanArray 5000XL Reader (Perkin Elmer, Boston, MA).
|
| Description |
n/a
|
| Data processing |
After the array slides were scanned, the resulting images were loaded into TIGR Spotfinder software (http://www.tigr.org/software/) and overlaid. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, and the intensity values of each spot were determined. Signal intensities of individual channels from an array slide were averaged and normalized using an array data analysis software (MIDAS) by using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis.
|
| |
|
| Submission date |
Mar 05, 2009 |
| Last update date |
Mar 05, 2009 |
| Contact name |
Yung-Hua Li |
| E-mail(s) |
[email protected]
|
| Phone |
902-494-3063
|
| Fax |
902-494-6621
|
| Organization name |
Dalhousie University
|
| Department |
Applied Oral Sciences
|
| Lab |
Biofilm Ecology and pathogenesis
|
| Street address |
5981 University Ave. Rm5215
|
| City |
Halifax |
| State/province |
NS |
| ZIP/Postal code |
B3H 3J5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8255 |
| Series (1) |
| GSE15125 |
Acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation |
|
