|
| Status |
Public on Feb 03, 2023 |
| Title |
CTR-W83-1 |
| Sample type |
RNA |
| |
|
| Source name |
Porphyromonas gingivalis W83
|
| Organism |
Porphyromonas gingivalis W83 |
| Characteristics |
genotype: wild type
treatment/time point: Fresh culture, Abs ~0.3
|
| Treatment protocol |
At OD600~0.3 time point, the bacteria cultures were stressed with Diethylamine (DEA) NONOate (15µl, 24mM stock concentration) for the NO stress studies. Untreated wild type and mutant strains cell cultures grown under the same conditions were used as controls. Samples were taken after 15 mins of NO stress treatment and controls were taken from untreated cultures at the same time.
|
| Growth protocol |
Fresh cultures of P. gingivalis strains (mutants and wild type) were grown from overnight cell cultures under anaerobic conditions at 37ºC in BHI broth. P. gingivalis strains were grown to early exponential phase (OD600:~0.3) in BHI broth under anaerobic conditions at 37ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh cultures using a total RNA isolation kit (Promega, WI). Additional DNase treatment was carried out using DNase kit (Ambion, Austin, TX). Samples from untreated cultures of P. gingivalis W83 were processed similarly and used as controls. RNA quality was checked using Agilent Bioanalyzer and Agilent RNA 6000 Nano.
|
| Label |
Cy3
|
| Label protocol |
cDNA (0.5 to 1 ug) was used to start the amplification and labeling reaction using a NimbleGen one-color labeling kit, in which Cy3 was randomly incorporated into the newly synthesized DNA by the Klenow fragment.
|
| |
|
| Hybridization protocol |
Labeled cDNA(2ug) derived from each RNAsample was hybridized with each array for over 16 to 18 h. The slides and arrays were washed and spun dry.
|
| Scan protocol |
The slides were scanned with a Roche MS200 microarray scanner with a resolution of 2 um.
|
| Data processing |
The normalization was done with the NimbleScan 2.6.0.0 built-in normalization function. Microarray data analysis was performed with a Partek Genomics suite (v6.5)
Differentially expressed genes were determined using fold-change (≥1.25) plus p (≤ 0.05) with FDR = 0.05.
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| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Marie-Claire Boutrin |
| Organization name |
Oakwood University
|
| Street address |
7000 Adventist Blvd NW
|
| City |
Huntsville |
| ZIP/Postal code |
35896 |
| Country |
USA |
| |
|
| Platform ID |
GPL18755 |
| Series (2) |
| GSE224064 |
The involvement of CdhR in Porphyromonas gingivalis during Nitric Oxide stress [microarray] |
| GSE224067 |
The involvement of CdhR in Porphyromonas gingivalis during Nitric Oxide stress |
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