|
| Status |
Public on Oct 31, 2017 |
| Title |
Substantia nigra from intact, levodopa-treated adult male Sprague Dawley rat, biological rep #1 |
| Sample type |
RNA |
| |
|
| Source name |
Intact, levodopa treated substantia nigra
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague Dawley
gender: Male
age: Adult
tissue: Substantia nigra
lesion: Saline
treatment: Levodopa
animal id: 10
|
| Treatment protocol |
Rats were anesthetized with 0.3ml/100g chloralpent. Each rat received two injections of 6-OHDA hydrobromide (Sigma-Aldrich, St. Louis, MO), 5ug/ul in 0.2% ascorbic acid in 0.9% saline, or vehicle (0.2% ascorbic acid in 0.9% saline). The two injection coordinates were AP+1.6mm, ML+2.4mm, DV -4.2, and, AP+0.2mm, ML+2.6mm, DV-7.0mm.
|
| Growth protocol |
Male, Sprague Dawley rats weighing between 200-225g were given access to food and water ad libitum. They were housed in an AALAC accredited animal facility in a reverse light-dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rats were sacrificed, brains frozen in isopentane for 30 seconds and stored individually at -80˚C. Structures were dissected using punches at -20˚C in a cryostat. Punches were ejected into an eppendorf tube containing Trizol and gently homogenized using a disposable plastic pestle. Samples were stored at -80˚C. RNA was isolated from Trizol homogenate using RNA Clean and Concentrator kit (Zymo). Quality of total RNA was determined on an Agilent Bioanalyzer. Only samples with RIN values ≥ 7 were used in this study.
|
| Label |
Biotin
|
| Label protocol |
Biotin labeled, cRNA was made using Ambion WT Expression kit (Life Technologies) combined with the GeneChip WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
2.5 ug of fragmented cRNA was hybridized for 17 hours at 45C in the GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained in the Fluidics Station 450 (Affymetrix) using fluidix protocol FS450-0007.
|
| Scan protocol |
GeneChips were scanned in a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
10G_LD+_Intact
0.5mm X 1.5 mm punch from substantia nigra
|
| Data processing |
Data processing and analysis were performed (N = 3 rats per experimental group) using R v3.2.3 (http://www.R-project.org) and Bioconductor (19). CEL files were imported into R, assessed for quality, and Robust-Multi Array (RMA) normalized at the probeset level using the oligo package (v1.34).
probe group file: Bioconductor package pd.ragene.1.0.st.v1 (version 3.14.1) (target = probeset)
meta-probeset file: Bioconductor package pd.ragene.1.0.st.v1 (version 3.14.1) (target = probeset)
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| |
|
| Submission date |
Oct 13, 2016 |
| Last update date |
Oct 31, 2017 |
| Contact name |
Jack W Lipton |
| E-mail(s) |
jack.lipton@hc.msu.edu
|
| Phone |
616-234-0950
|
| Organization name |
Michigan State University
|
| Department |
TSMM
|
| Street address |
333 Bostwick Ave.
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL10741 |
| Series (1) |
| GSE88726 |
Aberrant striatal but not nigral gene expression profiles are specifically associated with dyskinesia behavior following levodopa treatment in the 6-hydroxydopamine lesioned rat |
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