|
| Status |
Public on Jun 01, 2012 |
| Title |
Yoked Saline STR (1901185011_G) |
| Sample type |
RNA |
| |
|
| Source name |
dorsal striata
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
weight: 375±50g
tissue: dorsal striata
treatment: yoke saline
|
| Treatment protocol |
Male Sprague-Dawley rats (Charles River, Raleigh, NC), weighing 350-420 g, were housed individually under a reversed lighting 12-h light/dark cycle (lights on at 7:00 pm) with free access to food and water. All animal procedures were performed according to the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Animal Care and Use Committee of NIDA-IRP (ASP #09-BNRB-31)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Separate groups of rats were euthanized at 2 h, 24 h and 1 month after the last METH self-administration session. Dorsal striata were dissected from the brains and stored at -80ºC. Western blot experiments were conducted as described previously. Proteins were extracted from individual samples by sonication of the tissue in lysis buffer A (10 mM HEPES, 10mM KCl, 1.5 mM MgCl2, 1% Igepal CA) containing protease and phosphatase inhibitors (Roche Diagnostics) and centrifugation at 14 000g for 5 min at 4oC. Total RNA was isolated from the samples using RNeasy Mini Kit (QIAGEN, Valencia, CA). RNA concentration and integrity was determined using Agilent BioAnalyzer (Agilent, Santa Clara, CA). Samples were stored at -80ºC.
|
| Label |
biotin
|
| Label protocol |
600 ng of total RNA from each sample was amplified using Illumina RNA Amplification kit (Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics, Indianapolis, IN).
|
| |
|
| Hybridization protocol |
Microarray hybridization was done using RatRef-12 Expression BeadChips arrays (22 523 probes) (Illumina Inc., San Diego, CA). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55°C overnight according to the Gene Expression Protocol for BeadStation (Illumina Inc.). Hybridized cRNA was detected with cyanine3-streptavidin (GE Healthcare, Piscataway, NJ) and quantified using Illumina's BeadStation 500GX scanner.
|
| Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
|
| Description |
1901185011_G
Yoked Saline STR
|
| Data processing |
The microarray data reported in the manuscript are in accordance with MIAME guidelines. Gene expression changes caused by METH self-administration were analyzed using GeneSpring 11.0.2 software (Silicon Genetics, Redwood City, CA). Raw data were transformed using median normalization followed by unpaired t test. Functional annotation and gene classification analyses for significantly changed genes were performed using DAVID Annotation Tool (http://david.abcc.ncifcrf.gov)16 and were supported by literature searches. To concentrate on changes that could be related to gene function, we included only genes classified using DAVID Annotation Tool in further analyses and excluded all undefined (LOC and RGD) genes. Microarray results were extensively validated by qRT-PCR as described in the manuscript.
|
| |
|
| Submission date |
May 24, 2012 |
| Last update date |
Jun 01, 2012 |
| 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) |
| GSE38223 |
pCREB-dependent transcriptional activation is a mediator of molecular neuroadaptations induced by methamphetamine self-administration in the rat dorsal striatum |
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