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Chunk #7 — Materials and Methods — mRNA quantification by TaqMan® low density array

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Neuroadaptations in human chronic alcoholics: dysregulation of the NF-kappaB system.
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RNA preparation was performed using RNeasy Lipid Tissue Mini Kit (QIAGEN, Maryland, USA). RNA was quantified by Nanodrop® and Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to control RNA quality. Only RNA with clear ribosomal RNA, 18S and 28S, was used for further analysis. cDNA was synthesized with the High Capacity cDNA Archive Kit (Applied Biosystems, Foster City, CA). mRNA levels were quantified by TaqMan® Low Density Arrays (Applied Biosystems, Foster City, CA). In a pre-prepared micro fluidic card containing probes and primers for each gene, cDNA and TaqMan® Universal PCR Master Mix (Applied Biosystems) was added in a final concentration of 65 pg cDNA per sample and gene. Every sample was run in duplicate on the same array for each gene. The PCR amplification was performed at 50°C for 2 min, 94. 5°C for 10 min and 40 cycles of 97°C for 30 seconds followed by 59.7°C for 1 min. To measure the quantity of a given RNA species, the threshold cycles (Ct) were monitored by the Applied Biosystems 7900HT Fast Real-Time PCR System. Each mRNA expression