|
| Status |
Public on Mar 15, 2012 |
| Title |
Young liver 20 hr (Nov 2009) |
| Sample type |
RNA |
| |
|
| Source name |
5 month old n = 3
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
strain: C57BL/6J
tissue: liver
time of euthanasia: 20 hr
|
| Treatment protocol |
Five days prior to the experiment, animals were housed in a controlled dim (red) light setting with ad libitum chow food access. Groups of n = 3 mice from each age group were harvested at 3 hr intervals over a 24 hr period for tissues (brown fat, inguinal fat, liver). Tissues were flash frozen in liquid nitrogen at the time of harvest and frozen at -80 degrees C until processed.
|
| Growth protocol |
Male C57BL/6 mice were aged for periods of 5 or 24 months under 12 hr light: 12 hr dark conditions with ad libitum access to a chow diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriReagent (MRC, Cincinnati OH) in accordance with the manufacturer’s recommendations.
|
| Label |
biotin
|
| Label protocol |
The Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791) was used to create labeled cRNA from 750ng of input total RNA according to the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
MouseWG-6 v2 Beadchip (Illumina Sentrix Beadchip Array #11278593) were hybridized for 18 hrs at 58 degrees C with 1.5 micrograms of labeled cRNA.
|
| Scan protocol |
Data was scanned using an Illumina BeadArray Reader (Illumina, Inc., San Diego, CA)
|
| Data processing |
Metrics files from the bead scanner were checked to ensure that all samples fluoresced at comparable levels before importing samples into BeadStudio (Framework version 3.1.1.0) Gene Expression module v.3.2. Reference, hybridization control, stringency and negative control genes were checked for proper chip detection. Two datasets were created and exported for downstream analysis. Each contained the average signal for each transcript and the detection p-value. Both data sets had background subtracted from the transcript signals. One data set was quantile normalized and the other was not normalized.
We have applied Benjamini-Hochberg procedure (Benjamini 1995) (p<0.05) for FDR control in analysis of differential expression between age cohorts. Since we interpret and discuss differential genes in the context of their molecular function and gene interaction neighborhood we apply FDR to adjust the discovery of statistically significant biological pathways.
|
| |
|
| Submission date |
Nov 13, 2010 |
| Last update date |
Mar 15, 2012 |
| Contact name |
Jeffrey Gimble |
| E-mail(s) |
Jeffrey.M.Gimble.77@alum.dartmouth.org
|
| Phone |
(225) 763-3171
|
| Organization name |
Pennington Biomedical Research Center
|
| Lab |
Stem Cell Biology
|
| Street address |
6400 Perkins Rd
|
| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70808 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE25323 |
Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver (Nov 2009 dataset) |
| GSE25325 |
Biological Aging and Circadian Mechanisms in Murine Brown Adipose Tissue, Inguinal White Adipose Tissue, and Liver |
|
