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| Status |
Public on Jun 21, 2014 |
| Title |
Time Course of Gene Expression in the Substantia Nigra in Response to Intrastriatal 6-hydroxydopamine in the rat. |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
The 6-hydroxydopamine (6OHDA) rat model of parkinsonism is among the first, and most commonly used, animal models of Parkinson’s disease. It provides insight into the compensatory changes that occur in the brain after dopamine (DA) neuron degeneration. In order to better define the consequences of substantia nigra DA neuron loss on the neural and glial populations during and following nigrostriatal degeneration, tissue was collected and evaluated from the substantia nigra of 6OHDA or vehicle treated, or naïve rats at 1, 2, 4, 6 & 16 weeks.
Comprehensive gene expression analysis was conducted to detect significant differences in gene expression. Comparisons were conducted within the same treatment groups over time as well as across treatments within the same post-treatment interval. Longitudinal expression patterns were parsed using a k-means clustering algorithm as a method for finding patterns indicative of neuronal loss, upregulation in response to lesion or surgical damage exclusive of lesion.
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| Overall design |
Tissue was collected from the substantia nigra of 6OHDA treated, sham and naïve rats at 1, 2, 4, 6 & 16 weeks post-treatment. A unilateral striatal lesion was employed that results in a 99% striatal DA reduction and an 80% loss of DA neurons in the substantia nigra. 6OHDA lesions were confirmed via catecholamine quantitation by HPLC. RNA integrity was assessed with an Agilent 2100 Bioanalyzer with minimum RIN acceptance criteria of 8.0. Multidimensional plots and Pearson Correlations were used to establish group/treatment homogeneity. Tissue was subjected to comprehensive gene expression analysis using the Affymetrix Rat Gene 1.0ST array.
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| Contributor(s) |
Lipton JW, Collier TJ, Kanaan NM, Cole-Strauss A, Sortwell CE, Steece-Collier KA, Manfredsson FP, Mattingly Z, Tolod-Kemp EG |
| Citation(s) |
25992874 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P50 NS058830 |
Aging and Parkinson's Disease: Models of Therapeutics and Neurologic Comorbidity: Adminstrative Core: Induction of dopamine system plasticity by grafted undifferentiated neural progen |
MICHIGAN STATE UNIVERSITY |
Collier |
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| Submission date |
Jun 20, 2014 |
| Last update date |
Sep 22, 2016 |
| Contact name |
Jack W Lipton |
| E-mail(s) |
[email protected]
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| Phone |
616-234-0950
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| Organization name |
Michigan State University
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| Department |
TSMM
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| Street address |
333 Bostwick Ave.
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platforms (1) |
| GPL6247 |
[RaGene-1_0-st] Affymetrix Rat Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (33)
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| GSM1417196 |
Wk1, SN,6-OHDA,Rep1 |
| GSM1417197 |
Wk1, SN,6-OHDA,Rep2 |
| GSM1417198 |
Wk1, SN,6-OHDA,Rep3 |
| GSM1417199 |
Wk2, SN,Vehicle,Rep1 |
| GSM1417200 |
Wk2, SN,Vehicle,Rep2 |
| GSM1417201 |
Wk2, SN,Vehicle,Rep3 |
| GSM1417202 |
Wk2, SN,6-OHDA,Rep1 |
| GSM1417203 |
Wk2, SN,6-OHDA,Rep2 |
| GSM1417204 |
Wk2, SN,6-OHDA,Rep3 |
| GSM1417205 |
Wk4, SN,Vehicle,Rep1 |
| GSM1417206 |
Wk4, SN,Vehicle,Rep2 |
| GSM1417207 |
Wk4, SN,Vehicle,Rep3 |
| GSM1417208 |
Wk4, SN,6-OHDA,Rep1 |
| GSM1417209 |
Wk4, SN,6-OHDA,Rep2 |
| GSM1417210 |
Wk4, SN,6-OHDA,Rep3 |
| GSM1417211 |
Wk6, SN,Vehicle,Rep1 |
| GSM1417212 |
Wk6, SN,Vehicle,Rep2 |
| GSM1417213 |
Wk6, SN,Vehicle,Rep3 |
| GSM1417214 |
Wk6, SN,6-OHDA,Rep1 |
| GSM1417215 |
Wk6, SN,6-OHDA,Rep2 |
| GSM1417216 |
Wk6, SN,6-OHDA,Rep3 |
| GSM1417217 |
Wk16, SN,Vehicle,Rep1 |
| GSM1417218 |
Wk16, SN,Vehicle,Rep2 |
| GSM1417219 |
Wk16, SN,Vehicle,Rep3 |
| GSM1417220 |
Wk16, SN,6-OHDA,Rep1 |
| GSM1417221 |
Wk16, SN,6-OHDA,Rep2 |
| GSM1417222 |
Wk16, SN,6-OHDA,Rep3 |
| GSM1417223 |
Intact,SN,Rep1 |
| GSM1417224 |
Intact,SN,Rep2 |
| GSM1417225 |
Intact,SN,Rep3 |
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| Relations |
| BioProject |
PRJNA253211 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58710_RAW.tar |
144.5 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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