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Chunk #11 — Methods — RNA expression analysis

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FKBP5 variation is associated with the acute and chronic effects of nicotine.
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yes

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For a subset of laboratory subjects (N=48) whole blood was collected into PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) for RNA analysis. All experimental sessions began at 0800 and blood for RNA analysis was collected immediately prior to saline infusion for all subjects. RNA was extracted with the PaxGene Blood miRNA Kit (Qiagen, Hilden, Germany). The RNA quality was checked with an Agilent Bioanalyzer and the average RNA Integrity Number was 8.7 (range=6.2-9.9). An additional purification step was performed with the RNeasy MinElute Cleanup kit (Qiagen) to reduce salt concentrations. RNA was prepared for hybridization to HumanHT-12 v4 arrays at the Yale Center for Genome Analysis (YCGA) using the Illumina TotalPrep RNA Amplification kit (Life Technologies/Ambion, Foster City, CA). After hybridization, the arrays were scanned with a Bead Array Reader (Illumina, San Diego, CA, USA). Gene-level expression values were cubic-spline normalized using BeadStudio software (Illumina, San Diego, CA, USA). All subjects had FKBP5 expression values above a threshold detection level of p<0.00001. RNA expression was analyzed using mixed models as described above for genotype. To validate the array-based FKBP5 expression