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Chunk #11 — Methods — Subcellular fractionation and Western blot analysis

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Kalrn promoter usage and isoform expression respond to chronic cocaine exposure.
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Adult male mouse nucleus accumbens, dorsal striatum and cortical punches were sonicated and boiled in 1% SDS, 50 mM Tris [pH 7.4], 5 mM EDTA, 50 mM NaF, 2 mM sodium orthovanadate, 1 mM PMSF and protease inhibitor cocktail [17]. For subcellular fractionation studies, whole striatum was homogenized, fractionated by differential centrifugation followed by sucrose gradient centrifugation and extraction with TX-100, and subjected to Western blot analysis. Where indicated, blots were quantified using Gene Tools (Syngene, Frederick, MD) [12,17,33]. Gels were loaded with equal protein using a Bicinchoninic Acid Assay and bovine serum albumin standard to determine protein concentrations (Pierce, Rockford, IL). Commercially available mouse monoclonal antibodies were used: βIII tubulin (TUJ1; Covance), NR2B (clone N59/20; NeuroMab), Cdk5 (Santa Cruz Biotechnology) and Rac1 (Transduction Labs; also 23A8, Millipore).