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Chunk #9 — Materials and Methods — Reverse Transcription- Quantitative Polymerase Chain Reaction (RT-qPCR)

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GABRA2 Alcohol Dependence Risk Allele is Associated with Reduced Expression of Chromosome 4p12 GABAA Subunit Genes in Human Neural Cultures.
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Neural cultures 12–17 weeks post-plating were mechanically harvested and RNA extracted using TRIzol (Life Technologies, Carlsbad, CA). RNA concentrations were determined using a NanoDrop 2000 spectrophotometer (Thermo Fischer Scientific, Pittsburgh, PA) and cDNA was synthesized using a High Capacity cDNA Reverse Transcription kit (Life Technologies) using 2 µg of total RNA. Relative transcript levels represented in the resulting cDNA were measured by real-time qPCR using an Applied Biosystems 7500 instrument and FAM-labeled TaqMAN Assays (Life Technologies) for: GABRA1 (Hs00971228_m1), GABRA2 (Hs00168069_m1), GABRA4 (Hs00608034_m1), GABRB1 (Hs00181306_m1), GABRG1 (Hs00381554_m1), GABRG2 (Hs00381554_m1), GABRD (Hs00181309_m1), RBFOX3 (Hs01370653_m1), GAD2 (Hs00609534_m1), and SLC17A7 (Hs00220404_m1). VIC-labeled GUSB (β–glucuronidase, 4326320E) was used as a within-well reference gene for normalization. Each sample was assayed in triplicate and a standard curve using cDNA generated from mature iPSC-derived neural cells from one subject was included on each qPCR assay plate to allow pooling of relative RNA expression levels among all samples. CT values for target genes and the internal reference gene were converted to relative expression levels using the standard curve method, which compares each experimental sample with a calibrator reference