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Chunk #11 — Materials and methods — Quantitative real-time RT-PCR

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GABA-A and NMDA receptor subunit mRNA expression is altered in the caudate but not the putamen of the postmortem brains of alcoholics.
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identification of a single peak in the melting curve and a single band with the expected size on an agarose gel. All samples were run in duplicate and the primers covered all available transcripts for that specific gene. Primer efficiency was not examined further as all PCR products were shorter than 200 base pairs. Amplification was performed in 384-well optical plates using the ABI PRISM 7900HT Sequence Detection System (Applied Biosystems) with an initial denaturation of 5 min at 95°C, followed by 45 cycles of 95°C for 15 s, 60°C for 30 s, and 72°C for 30 s. A melting curve was determined at the end of cycling to ensure the amplification of a single PCR product. Cycle threshold values (Ct) were determined with the SDS 2.4 and RQ Manager 1.2 softwares supplied with the instrument. The expression of each target gene relative to a normalization factor was calculated with Data Assist v2.0 using the 2−ΔCt method as previously described (Schmittgen and Livak, 2008). Reference gene beta actin (ACTB) for putamen (expression stability value M = 0.35) and caudate (expression stability value M = 0.42) was selected for normalization according to previously developed approach for analysis of reference genes (Johansson