|
| Status |
Public on Sep 14, 2017 |
| Title |
P_gingivalis_PG0162PG1660-AN_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Porphyromonas gingivalis PG0162- PG1660 mutant
|
| Organism |
Porphyromonas gingivalis W83 |
| Characteristics |
genotype/variation: PG10162 and PG1660 double deletion mutant
|
| Treatment protocol |
Porphyromonas gingivalis were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media. One group was kept under anaerobic conditions, and another group was stressed by 0.25 mM of hydrogen peroxide for 15 min . McKenzie et al., Microbiology, 158(Pt 10):2465-79.
|
| Growth protocol |
Porphyromonas gingivalis cultures were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media (Dou et al. FEMS Micro Lett. 312(1):24-32).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using SV Total RNA Isolation system (Promega); cDNA was synthesized by using Transcriptor High Fidelity cDNA Synthesis kit (Roche). Dou et al., Journal of Bacteriology, 196(23):4057-70.
|
| Label |
Cy3
|
| Label protocol |
Cyanine dyes Cy3 (Amersham Biosciences) was used to label the sample cDNA.
|
| |
|
| Hybridization protocol |
Slides were hybridized in hybridization buffer containing labelled probed for 16-20 hrs and then washed in 2×SSC/0.1%SDS, 0.1×SSC/0.1%SDS, 0.1×SSC and ddH2O to remove non-specific binding.
|
| Scan protocol |
The slides were scanned using ScannArray 4000 scanned (GSI Lumonics) and the images were acquired by using ScanArray software.
|
| Description |
PG0162PG1660 mutant microarray.xlsx
This sample is of Porphyromonas gingivalis PG0162-PG1660 deletion mutant under anaerobic conditions. It is the first of three mutant biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The data were subquently analyzed using c5B Quantarray software (Version 2.0) and normalized. The raw data (.pair file) was subjected to RMA then using GeneSpring software (Silicon Genetics) to analyze. McKenzie et al., Microbiology, 158(Pt 10):2465-79.
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| |
|
| Submission date |
Sep 13, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Yuetan Dou |
| E-mail(s) |
[email protected]
|
| Organization name |
Loma Linda University
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
11021 Campus Street AH114
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92354 |
| Country |
USA |
| |
|
| Platform ID |
GPL6533 |
| Series (2) |
| GSE103838 |
Expression profiling analyses of ECF sigma factor PG1660 mutant of Porphyromonas gingivalis W83 |
| GSE103839 |
Expression profiling analyses of ECF sigma factor of Porphyromonas gingivalis W83 |
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