|
| Status |
Public on Dec 31, 2008 |
| Title |
Healthy control saliva-10 |
| Sample type |
RNA |
| |
|
| Source name |
saliva
|
| Organism |
Homo sapiens |
| Characteristics |
healthy control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Twelve pancreatic cancer samples and 12 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMAX Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).
After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
|
| Scan protocol |
Standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)
|
| Description |
no additional information
|
| Data processing |
The CEL files from all datasets (array data from 12 pancreatic cancer saliva samples and 12 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.
|
| |
|
| Submission date |
Dec 30, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Lei Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
UCLA Dental Research Institute
|
| Street address |
10833 Le Conte Ave., CHS 73-029
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90066 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE14245 |
Multiple Salivary Biomarkers for Early Detection of Pancreatic Cancer |
|
| Relations |
| Reanalyzed by |
GSE119087 |
