|
| Status |
Public on May 17, 2023 |
| Title |
405-3 |
| Sample type |
RNA |
| |
|
| Source name |
Wild type
|
| Organism |
Treponema denticola ATCC 35405 |
| Characteristics |
strain: ATCC 35405
|
| Treatment protocol |
Td 35405 T. denticola ATCC 35405 grown in medium containing 10% serum Td YM-3 T. denticola YM-3 grown in medium containing containing 10% serum
|
| Growth protocol |
T. denticola ATCC 35405, DMSP3 or K1 were inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 d (to an absorbance at 660 nm of approximately 0.4-0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using TRIzol Reagent (nitrogen) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
The cRNA was amplified, labeled using Low Input Quick Amp WT Labeling Kit according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 15K 60-mer oligomicroarray (Treponema denticola custom Microarray 8x16K; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction 12.0.3.1(Agilent Technologies).
|
| Data processing |
The fluorescent intensity data extracted from the raw images were imported into Agilent Feature Extraction 12.0.3.1 (Agilent Technologies). After per chip normalization (Shift to 75 percentile) and per gene normalization (mean of control samples) were performed with GeneSpring 13.1.1.
|
| |
|
| Submission date |
Sep 15, 2022 |
| Last update date |
May 17, 2023 |
| Contact name |
Kazuyuki Ishihara |
| E-mail(s) |
ishihara@tdc.ac.jp
|
| Phone |
81-3-6380-9558
|
| Organization name |
Tokyo Dental College
|
| Department |
Microbiology
|
| Street address |
2-1-14 Kanda-Misakicho, Chiyoda-ku
|
| City |
Tokyo |
| ZIP/Postal code |
101-0061 |
| Country |
Japan |
| |
|
| Platform ID |
GPL29234 |
| Series (1) |
| GSE213450 |
Localization and pathogenic role of the cysteine protease dentipain in Treponema denticola |
|
