|
| Status |
Public on Sep 17, 2005 |
| Title |
Age alters the gene expression profiles of rat oculomotor nucleus and spinal cord |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
|
| Summary |
Some of the most common neurodegenerative disorders have a strong association with aging. Curiously, these conditions tend to involve specific areas of the central and peripheral nervous system, at least initially. For example, amyotrophic lateral sclerosis preferentially targets spinal motor neurons and spares oculomotor neurons. This suggests that aging has divergent effects on brain stem and spinal cord, a factor that may explain differential susceptibility to certain neurodegenerative disorders. Therefore, for this study we asked whether aging induces a change in the evolution of the transcriptome of oculomotor nucleus (OMN) throughout the lifespan which would be different than that of the spinal cord aging. Age induced a transcriptome shift to a pattern consistent with inflammation/immune response in both OMN and spinal cord. However, the response was more dramatic in the spinal cord. On the other hand, age repressed genes coding ion channels and transporters in OMN and cytoskeletal proteins in the spinal cord. The results indicate that OMN and spinal cord transcriptomes change differently with age. The results give an initial glimpse of how tissue-specific gene expression patterns may underlie the differential susceptibility to age-related neuromuscular dysfunction.
Keywords: time course, aging
|
| |
|
| Overall design |
Total RNA was obtained with TRIzol (Invitrogen Carlsbad, CA) following the manufacturers recommended protocol. Tissues from 4 animals were combined into each RNA sample to decrease inter-subject variability. Biotinylated cRNA samples were hybridized to Affymetrix Rat Genome RA230 gene chips (n=18 chips) described previously [McMullen et al. 2004]. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Comparisons used the 6-mo transcriptome as the baseline and the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/ decrease” difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.70 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.
|
| |
|
| Contributor(s) |
McMullen CA, Andrade FH, Gamboa J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Sep 14, 2005 |
| Last update date |
Mar 03, 2017 |
| Contact name |
Colleen A McMullen |
| E-mail(s) |
[email protected]
|
| Phone |
859-323-9443
|
| Fax |
859-323-1070
|
| Organization name |
University of Kentucky
|
| Department |
Physiology
|
| Street address |
800 Rose St MS508
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40536 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL341 |
[RAE230A] Affymetrix Rat Expression 230A Array |
|
| Samples (18)
|
| GSM74333 |
6 month oculomotor nucleus rep 1 |
| GSM74334 |
6 month oculomotor nucleus rep 2 |
| GSM74335 |
6 month oculomotor nucleus rep 3 |
|
| Relations |
| BioProject |
PRJNA92819 |
Less...
More...