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Chunk #38 — Materials and Methods — Quantitative real-time RT-PCR analysis

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Broad epigenetic signature of maternal care in the brain of adult rats.
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The expression patterns of 45 transcripts examined by microarray were quantified. For genes shown in Figure 1c (also see Table S1) primer design (Table S2) and analysis were performed by Genome Quebec (ABI lightcycler, ABI biosystems), whereby the expression of an additional 7 housekeeping genes (Actb, Gapdh, Gusb, Pum1, Rpl19, Rps18, Tubb5) was assessed for the same subjects used for microarray hybridization. The gene showing the least variance between High and Low LG adult offspring was selected as the reference gene for all subjects (GusB), and statistical significance, fold differences and standard errors of the mean were calculated according to published methods using the freely-available Relative Expression Software Tool program[56]. For the quantification of gene expression differences related to the NR3C1 gene shown in Figure 4b and the Pcdh gene clusters shown in Figure 5 (also see Table S1), a standard curve was generated from 7 serial dilutions of a mixture of cDNA from each High and Low LG offspring, and gene expression was quantified relative to the tubulin housekeeping gene (480 lightcycler, Roche) for an additional cohort of 8