|
| Status |
Public on Aug 15, 2013 |
| Title |
Human saliva microbiota from healthy adult_H111 |
| Sample type |
genomic |
| |
|
| Source name |
Human saliva microbiota_healthy
|
| Organism |
human oral metagenome |
| Characteristics |
gender: male
age: 20
dmft index: 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Two milliliters of saliva were collected from each human-host individual into a tube containing an equal volume of lysis buffer and followed by DNA extraction
|
| Label |
Cy5
|
| Label protocol |
DNA was labeled with the fluorescent dye Cy5 (GE Healthcare) by random priming
|
| |
|
| Hybridization protocol |
DNA was suspended in hybridization buffer and then kept at 65°C until hybridization. Hybridizations were performed at 42°C for 10 h using a Tecan HS4800 Pro hybridization station
|
| Scan protocol |
Arrays were scanned with a ScanArray 500 microarray scanner at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%.
|
| Data processing |
The data processing and analysis was carried out by the IEG microarray manager available at http://ieg.ou.edu/microarray/, which is a data analysis pipeline specifically designed for functional gene arrays such as GeoChip and HuMiChip etc.
Data was filtered by SNR<=2, minimal signal intensity>=1000, resulting incomplete/subset data matrix (Probes which did not meet these criteria were not considered as detected in the study).
Signal intensity were normalized by CORS universal standard probes (Liang et. al 2010 AEM), probes with SNR<2 are removed, all data was log transformed and mean ratio was calculated for further statistical analysis
We used minimal signal intensity of 1000 and SNR (Signal to Noise Ratio) cutoff of 2 for positive callings of the presence of a gene
|
| |
|
| Submission date |
Aug 14, 2013 |
| Last update date |
Aug 15, 2013 |
| Contact name |
Qichao Tu |
| E-mail(s) |
philloid@gmail.com
|
| Organization name |
University of Oklahoma
|
| Street address |
101 David L Boren Blvd
|
| City |
Norman |
| State/province |
OK |
| ZIP/Postal code |
73019 |
| Country |
USA |
| |
|
| Platform ID |
GPL17575 |
| Series (1) |
| GSE49875 |
HuMiChip analysis of Saliva microbiota |
|
