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Chunk #6 — Materials and Methods — Dissection of NAc Tissue, Sample Preparation, and ERRBS Pipeline

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Genome-Wide DNA Methylation Profiling Reveals Epigenetic Changes in the Rat Nucleus Accumbens Associated With Cross-Generational Effects of Adolescent THC Exposure.
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Samples were processed following procedures outlined in Supplementary Figure S1. Bilateral NAc tissue was dissected (15-gauge punch), from frozen brains of 32 F1 rats (PND~62) from adult offspring of parents with repeated exposure to either THC or VEH during adolescence (Szutorisz et al, 2014). Eight females and eight males from both the THC- and VEH-exposed lines were derived from five to six different mothers and fathers in each group. Genomic DNA was extracted (DNeasy Blood & Tissue Kit; Qiagen, Valencia, CA, USA) and ~250 ng DNA/sample was processed for ERRBS following established protocols (Akalin et al, 2012a). ERRBS sequencing libraries were constructed and sequenced on a HiSeq2000 (Weill Cornell genomics core facility, New York, NY). As per Alkalin et al (2012a), reads were aligned to an in silico bisulfite-converted version of the rn4 reference genome assembly using Bismark (Krueger and Andrews, 2011), allowing 2 bp mismatches per read, and discarding reads mapping to multiple locations.