|
| Status |
Public on Nov 28, 2013 |
| Title |
10 day old NOD-Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
age: 10 day old
Sex: female
strain: NOD/LtJ (NOD)
|
| Treatment protocol |
pancreatic islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion, and placed in Trizol Reagent.
|
| Growth protocol |
NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility. All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Micro Kit.
|
| Label |
Cy5
|
| Label protocol |
300 ng of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Pancreatic Islets (pool of 6 age-matched NOD.B10 mice)
|
| Organism |
Mus musculus |
| Characteristics |
age: 10 day old
Sex: Female
strain: NOD.B10Sn-H2b/J (NOD.B10)
|
| Treatment protocol |
pancreatic islets were isolated from individual NOD and NOD.B10 mice by collagenase digestion, and placed in Trizol Reagent.
|
| Growth protocol |
NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility. All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Micro Kit.
|
| Label |
Cy3
|
| Label protocol |
300 ng of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.
|
| Scan protocol |
Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)
|
| Description |
Biological replicate of gene expression in the isolated pancreatic islets of individual 10 day old NOD mice vs. a pool of age-matched NOD.B10 controls
|
| Data processing |
Data were processed using Genespring 11.5. Samples were filtered for detected entities.
|
| |
|
| Submission date |
Nov 27, 2013 |
| Last update date |
Nov 28, 2013 |
| Contact name |
Linda Yip |
| Organization name |
Stanford University
|
| Department |
Medicine
|
| Lab |
C.G. Fathman
|
| Street address |
269 Campus Drive West, CCSR Building Rm. 2240
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE52815 |
Gene expression in the isolated islets of 10 day old, 4 wk old, 12 wk old, and 20 wk old Non-Obese Diabetic (NOD) mice compared to healthy age matched control NOD.B10 mice |
|
