|
| Status |
Public on Jan 26, 2012 |
| Title |
Wildtype, independent set #1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Wild-type UA159, early phase
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
strain: UA159
genotype: wild-type
growth phase: early
|
| Growth protocol |
Grown to early phase (OD=0.3) in plain BHI broth, 37C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using hot phenol.
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA was labeled by following the protocols recommended by the Pathogen Functional Genomics Resource Center (PFGRC).
|
| |
|
| Channel 2 |
| Source name |
Wild-type UA159, mid-exponential phase
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
strain: UA159
genotype: wild-type
growth phase: mid-log
sample type: reference
|
| Growth protocol |
Grown to mid-log phase in BHI broth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using hot phenol.
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA was labeled by following the protocols recommended by the Pathogen Functional Genomics Resource Center (PFGRC).
|
| |
|
| |
| Hybridization protocol |
Hybridized at 37oC in the MAUI Hybridization System.
|
| Scan protocol |
Axon GenePix 4000B scanner.
|
| Description |
UA1
The BrpA mutant was grown similarly as the wild-type, but it does have defects in biofilm formation and stress tolerance response.
|
| Data processing |
After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software (http://www.tm4.org/spotfinder.html) and overlaid. A spot grid was created according to TIGR specifications and then manually adjusted to fit all spots within the grid. The intensity values of each spot were measured and saved into .mev and .tav files. Data were then normalized using LOWESS and iterative log mean centering with default settings, followed by in-slide replicate analysis using TIGR microarray data analysis software (MIDAS, http://www.tm4.org/midas.html). Spots that were flagged as bad because of either low intensity values or signal saturation were automatically discarded and labeled as null in the matrix. Statistical analysis was carried out using BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) and genes that were differentially transcribed were identified using the Group Comparison program at the statistical significance level of P < 0.001 and 0.01.
|
| |
|
| Submission date |
Jan 25, 2012 |
| Last update date |
Jan 26, 2012 |
| Contact name |
Zezhang Tom Wen |
| E-mail(s) |
[email protected]
|
| Phone |
5049418465
|
| Fax |
5049418319
|
| Organization name |
LSU Health Sciences Center
|
| Department |
Oral and Craniofacial Biology
|
| Lab |
Microbiology
|
| Street address |
1100 Florida Avenue
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70119 |
| Country |
USA |
| |
|
| Platform ID |
GPL15165 |
| Series (1) |
| GSE35349 |
BrpA-deficiency on the transcriptional profile in Streptococcus mutans during early exponential phase |
|
