|
| Status |
Public on Nov 13, 2009 |
| Title |
Aerobic vs anaerobic experiment 2, replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from whole bacteria
|
| Organism |
Porphyromonas gingivalis |
| Characteristics |
cell type: bacteria
strain: W83
|
| Growth protocol |
Bacterial cells were grown in the presence of 6% oxygen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA were primed with random DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion, Austin, TX). Dyes were incorporated into the reverse transcribed cDNAs (Cy3 and Cy5, GE Healthcare).
|
| |
|
| Channel 2 |
| Source name |
Total RNA from pooled whole bacteria
|
| Organism |
Porphyromonas gingivalis |
| Characteristics |
strain: W83
age: log phase
cell type: bacteria
|
| Growth protocol |
Bacterial cells were grown anaerobically.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA were primed with random DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion, Austin, TX). Dyes were incorporated into the reverse transcribed cDNAs (Cy3 and Cy5, GE Healthcare).
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA probes were combined and mixed with hybridization buffer and applied to prehybridized array. Array was placed in hybridization chamber and incubated ON at 42C.
|
| Scan protocol |
Scanned on an Axon 4200A microarray scanner.
Images were quantified using GenePix software (v 6.0).
|
| Description |
Biological replicate 2 of 3. Technical replicate 1.
|
| Data processing |
Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LIMMA was used. LIMMA ( Linear Models for Microarray Data) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted arrays such as normalization of cDNA data, and background subtraction.Data were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD). SAOPMD combines all the repeats within and between arrays and generates statistics. Data included were derived from five microarrays.
|
| |
|
| Submission date |
Sep 03, 2009 |
| Last update date |
Nov 13, 2009 |
| Contact name |
Janina P Lewis |
| E-mail(s) |
jplewis@vcu.edu
|
| Phone |
804-628-7014
|
| Organization name |
Virginia Commonwealth University
|
| Department |
Philips Institute of OCMB
|
| Lab |
Lewis
|
| Street address |
521 North 11th Street
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL9149 |
| Series (1) |
| GSE17960 |
Aerobic transcriptome of Porphyromonas gingivalis |
|
