|
| Status |
Public on Jan 16, 2019 |
| Title |
8 kinds of bacterial genomic DNA mixture_dilution_step0_n=1 |
| Sample type |
genomic |
| |
|
| Source name |
8 kinds of bacterial genomic DNA mixture_dilution_step0
|
| Organisms |
Treponema denticola; Aggregatibacter actinomycetemcomitans; Porphyromonas gingivalis; Fusobacterium nucleatum; Streptococcus gordonii; Streptococcus mutans; Tannerella forsythia; Prevotella intermedia |
| Characteristics |
sample type: 8 kinds of bacterial genomic DNA mixture_dilution_step0
|
| Treatment protocol |
Human dental plaque samples were collected from the erupted teeth of a person by brushing for 1 min with a sterile toothbrush. The plaques attached to the brush were removed by washing several times in 5 ml sterile distilled water in 15 ml test tubes then collected by centrifugation at 1,600×g for 20 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the samples using a Wizard Genome DNA Purification Kit (Promega).
|
| Label |
Cy5
|
| Label protocol |
Cy5 labeled PCR primer
|
| |
|
| Hybridization protocol |
Two hundred μl hybridization solution was prepared from the PCR products with 0.24 M Tris/HCl (pH 7.5), 0.24 M NaCl, and 0.05% Tween®20. Hybridization and washing were performed by DNA chip Instrument Systems (Mitsubishi Chemical Co., Ltd.) for 16 h, after which the DNA chips were further washed with wash solution (0.24 M Tris/HCl pH 7.5 and 0.24 M NaCl) for 5 min at room temperature.
|
| Scan protocol |
Hybridization signals were examined by Genopal Reader™ (Mitsubishi Chemical Co., Ltd.) with multi-beam excitation technology (Yokogawa Electric, Tokyo, Japan). Fluorescence signals were detected with exposure times of 0.1, 1, 4, and 40 s using this instrument, and the longest exposure images without saturated pixels in the spots were adopted as spot images and quantified as the fluorescence signal intensity per second.
|
| Description |
6 serial 16-fold dilutions of eight kinds of genomic DNA mixture solution.
|
| Data processing |
The probe signal intensity was determined from the fluorescence signal intensity. The mean and standard deviation of the fluorescence signal intensity of the background spot without the probe were calculated, and the sum of the mean and standard deviation of three repetitions was defined as the background signal intensity. Probe signal intensity was calculated by subtracting the background signal intensity from the median of the fluorescence signal intensity of the five spots of each probe.
BLANK array features are not represented in the data table.
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| |
|
| Submission date |
Jan 15, 2019 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Naoyuki Togawa |
| E-mail(s) |
togawa.naoyuki.ms@m-chemical.co.jp
|
| Phone |
+81-45-504-1139
|
| Organization name |
Mitsubishi Chemical Corporation
|
| Lab |
Tsurumi R&D Center
|
| Street address |
10-1,Daikokucho,Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0053 |
| Country |
Japan |
| |
|
| Platform ID |
GPL25612 |
| Series (1) |
| GSE125085 |
Method for absolute quantification of microbial communities by using both microarrays and competitive PCR |
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