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Chunk #10 — 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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Total RNA (200 ng) was reverse transcribed into cDNA in a 20 μl reaction mixture using Superscript III reverse transcriptase (Invitrogen). RT negative control was performed by omitting reverse transcriptase in the reaction in order to confirm no genomic DNA contamination in the isolated RNA. Real-time PCRs were performed in a 10 μl reaction mixture containing 4 μl cDNA (1 ng), 1 × PCR reaction buffer, 3 mM MgCl2, 0.3 mM dNTP, 1 × ROX reference dye, 0.8 U JumpStart Taq DNA polymerase (Sigma-Aldrich), 5 × SYBR Green I (Invitrogen), and 0.4 μM each of forward and reverse primers. The gene-specific primer pairs (primer sequences shown in Table S3 in Supplementary Material) were designed using database GETPrime, EPFL (Gubelmann et al., 2011) or Primer Express Software version 3.0 (Applied Biosystems) and then validated using hippocampal cDNA from human brain by 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