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Sample GSM596029 Query DataSets for GSM596029
Status Public on Sep 21, 2010
Title AVG_Signal-25 -CTR SAL a (6)
Sample type RNA
 
Source name Striatal Brain Tissue
Organism Rattus norvegicus
Characteristics treatment: Saline Control
strain: Sprague Dawley
Treatment protocol 6-OHDA lesioning. Unilateral lesions were performed under anesthesia with chloral hydrate (400 mg/kg, i.p.). After immobilization on a stereotaxic frame (model 940; David Kopf Instruments), a hole was drilled in the skull for injections of 6-OHDA in the medial forebrain bundle (MFB). 6-OHDA (2 µg/µl x 5 µl in 0.9% NaCl containing 0.2 mg/ml ascorbic acid) was unilaterally injected into the left medial forebrain bundle (-4.4 mm AP, 1.2 mm ML relative to bregma and 8.4 mm below skull) over 4 minutes. At the end of each injection, the micropipette was left in place for an additional 5 min and then withdrawn slowly to prevent reflux of the solution.
Growth protocol Animals. Male Sprague-Dawley rats (Charles Rivers Laboratories, Raleigh, NC), weighing g at the beginning of the experiments were used in the present study. Animals were housed in a humidity- and temperature-controlled room and were given free access to food and water. All animal procedures were performed according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.
Extracted molecule total RNA
Extraction protocol METH treatment and tissue collection. One week after measuring METH-induced rotation, the animals were divided into two groups based on METH-induced rotation. The two matched groups of animals were injected with either saline or METH (2.5 mg/kg, intraperitoneally) and then sacrificed two hours after the injection. Additional control animals that had not gotten 6-OHDA injections were also used. Their brains were quickly removed, tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used in HPLC, microarray, and quantitative PCR experiments. The experimental groups were: saline-treated controls (SC), METH-treated controls (MC), non-lesioned side of saline-treated 6-OHDA-injected rats (SNL), lesioned side of saline-treated 6-OHDA-injected rats (SL), non-lesioned side of METH-treated 6-OHDA-injected animals (MNL), and lesioned side of METH-treated 6-OHDA-injected animals (ML). HPLC. For monoamine analysis, the brain regions were homogenized in 0.01M HClO4 and centrifuged at 14, 000 x g for 15 min. DA, 3,4-dihydroxyphenylacetic acid (DOPAC), homovanillic acid (HVA), 5-HT and 5-hydroxyindoleacetic acid (5-HIAA) levels were analyzed in the brain tissue extracts using HPLC with electrochemical detector (Krasnova et al., 2007). RNA extraction. Total RNA was isolated using Qiagen RNeasy Midi kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and showed no degradation.
Label Cyanine3-streptavidin
Label protocol Brains were quickly removed, tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used in HPLC, microarray, and quantitative PCR experiments. The experimental groups were labelled as: saline-treated controls (SC), METH-treated controls (MC), non-lesioned side of saline-treated 6-OHDA-injected rats (SNL), lesioned side of saline-treated 6-OHDA-injected rats (SL), non-lesioned side of METH-treated 6-OHDA-injected animals (MNL), and lesioned side of METH-treated 6-OHDA-injected animals (ML).
 
Hybridization protocol Microarray hybridization. Microarray hybridization was carried out using Illumina’s RatRef-12 Expression BeadChips arrays (22, 523 probes) (Illumina Inc., San Diego, CA). In brief, a 600 ng aliquot of total RNA from each striatal sample was amplified using Ambion’s Illumina RNA Amplification kit (cat. no. IL1791; Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics GmbH, Mannheim, Germany, cat. no. 11388908910). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55 oC overnight according to the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Illumina Inc., San Diego, CA, cat. # 11201828).
Scan protocol Hybridized biotinylated cRNA was detected with Cyanine3-streptavidin (Amersham Biosciences, Piscataway, NJ, cat. #146065) and quantified using Illumina's BeadStation 500GX Genetic Analysis Systems scanner.
Description SAMPLE 24
Data processing The microarray data reported in the manuscript are in accordance with MIAME guidelines. The Illumina BeadStudio software was used to measure fluorescent hybridization signals. Data were extracted by BeadStudio (Illumina, San Diego, CA) and then analyzed using GeneSpring software v. 7.3.1 (Silicon Genetics, Redwood City, CA, USA). Raw data were imported into GeneSpring and normalized using global normalization. The normalized data were used to identify changes in gene expression in these 4 group comparisons. A gene was identified as changed if it showed increased or decreased expression according to an arbitrary cut-off of 1.7-fold changes at p < 0.025. In previous studies, genes identified by similar criteria were consistently validated by quantitative PCR (Krasnova et al., 2008; Cadet et al., 2009; Jayanthi et al., 2009).
 
Submission date Sep 20, 2010
Last update date Sep 20, 2010
Contact name Jean Lud Cadet
E-mail(s) jcadet@intra.nida.nih.gov
Organization name NIDA, IRP
Department Molecular Neuropsychiatry Research Branch
Lab Molecular Neuropsychiatry Section
Street address 251 Bayview Blvd, Suite 200
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6101
Series (1)
GSE24233 Transcriptome profiling in 6-hydroxydopamine hemiparkinsonian rats reveals methamphetamine-mediated dopamine-independent changes in striatal gene expression.

Data table header descriptions
ID_REF
VALUE average signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1356720 0.027224064 0.87758
ILMN_1355539 0.6671274 0.95394
ILMN_1365415 -0.28957653 0.99879
ILMN_1373448 -0.643167 0.99636
ILMN_1353631 -0.99761295 1
ILMN_2039365 0.8696761 0.99515
ILMN_1361828 0.2509532 1
ILMN_1371132 0.3792863 0.82788
ILMN_1374582 1.403966 0.79515
ILMN_1359915 0 0.6303
ILMN_1366207 0.36529303 0.98545
ILMN_1353331 -0.3623228 0.77333
ILMN_1353943 0.23516846 0.96242
ILMN_1366701 -0.320773 0.66545
ILMN_1357309 0 0.62667
ILMN_1350712 0.14807606 1
ILMN_1370136 0.2587917 0.95758
ILMN_1373899 0.32872868 1
ILMN_1360341 -0.7278228 0.96848
ILMN_1530174 0 0.38424

Total number of rows: 22523

Table truncated, full table size 618 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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