|
| Status |
Public on Jun 12, 2013 |
| Title |
Mouse Saliva tumor 1 |
| Sample type |
RNA |
| |
|
| Source name |
Tumor mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C56BL/6
tissue: saliva supernatant
sample group: mice with pancreatic tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the discovery of candidate pancreatic cancer-discriminatory salivary transcriptomic biomarkers, saliva RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer?s protocol. There were 30 mice each in the control and tumor group. Samples derived from 5 mice in each group were pooled for RNA extraction. Pooling was necessary to ensure that sufficient salivary mRNA was obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase. For microarray analysis, mRNA from mouse saliva was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices). After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3?-Amplification Reagents for labeling of transcripts (Affymetrix). The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning.
|
| Label |
biotin
|
| Label protocol |
After purification, cDNA were transcribed in vitro and biotinylated using GeneChip Expression 3′-Amplification Reagents for labeling of transcripts (Affymetrix).
|
| |
|
| Hybridization protocol |
The labeled RNAs (15 ug each) were subsequently fragmented and sent to the UCLA microarray core facility for array hybridization and scanning. The GeneChip Mouse Genome 430 2.0 Array, was used for profiling analysis
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
153931
|
| Data processing |
Arrays were analyzed using R 2.7.0 (http://www.r-project.org). The probe logarithmic intensity error estimation (PLIER) expression measures were computed after background correction and quantile normalization. Quantile normalization was performed across all samples to make the distributions similar and comparable among all probe sets. For every probe set, the 2-sample t-test was applied to identify differential expression between saliva samples obtained from pancreatic cancer-bearing mice and healthy mice. After obtaining the estimates and P-values for each probe set, we corrected the P-values for the false discovery rate. A score was then generated based on the corrected P-values and differential expression levels.
|
| |
|
| Submission date |
Jun 10, 2013 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Tristan Grogan |
| Organization name |
UCLA
|
| Street address |
911 Broxton Ave, 3rd floor
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90024 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE47811 |
Pancreatic cancer biomarkers in mouse saliva |
|
