|
| Status |
Public on Nov 03, 2006 |
| Title |
liver Control Standard Diet 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Normal Diet, Ad Lib, Liver
|
| Organism |
Mus musculus |
| Characteristics |
C57BL/6NIA Mice, 18months of age, Standard Diet, Ad Lib, Liver
|
| Treatment protocol |
Mice were fed AIN-93G Standard Diet, Ad Lib
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen RNEasy Columns
|
| Label |
Cy-3
|
| Label protocol |
Agilent low RNA Input Linear Amplification Kit using Cyanine-3-CTP
|
| |
|
| Channel 2 |
| Source name |
Standard Diet, Ad Lib, Liver, Pools of 5 samples
|
| Organism |
Mus musculus |
| Characteristics |
C57BL/6NIA Mice, 18months of age, Standard Diet, Ad Lib, Liver pools
|
| Treatment protocol |
Mice were fed AIN-93G Standard Diet, Ad Lib
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen RNEasy Columns and 5 samples were pooled
|
| Label |
Cy-5
|
| Label protocol |
Agilent low RNA Input Linear Amplification Kit using Cyanine-5-CTP
|
| |
|
| |
| Hybridization protocol |
17 hour incubation following Agilent protocols using 750ng of both Cy3 and Cy5 labeled material, In Situ Hybridization Kit reagents and control probes followed by a 10 minute room temperature wash in 6X SSC,0.005% tritonX-102 and 5 minutes at 4 degrees C in 0.1X SSC, 0.005% Triton X-102. The arrays were dried in a Nitrogen stream and scanned.
|
| Scan protocol |
Arrays were scanned using an Agilent Scanner G2565AA .
|
| Description |
liver Control Standard Diet 1
|
| Data processing |
Data from both channels was extracted using the Agilent Feature Extractor Software, Version 7.5. Due to potential variation of the Cy-5 dye we prefer to analyze the green channel alone and use single channel data. Results for control probes were first removed, multiple repeats of any probe were averaged, then each array was z-normalized. Differently expressed genes were identified between the 3 sample groups and pathway enrichment analysis was conducted using Diane 6.0, an in-house microarray analysis program.
Both the green channel and red channel raw data are available in the Supplementary file at the foot of the Sample record.
|
| |
|
| Submission date |
Oct 20, 2006 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL2872 |
| Series (1) |
| GSE6089 |
Expression patterns in liver after resveratrol treatment of mice on a high-calorie diet |
|
| Relations |
| Reanalyzed by |
GSE24950 |
