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Chunk #6 — Materials and methods — RNA-seq and genotyping

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Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.
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RNA was extracted from the brain tissues using the Qiagen RNeasy kit (Qiagen, Germantown, MD, USA). The RNA-seq samples were prepared using the TruSeq RNA Library Pre Kit v2 (Illumina, Inc., San Diego, CA, USA) and sequenced on the Illumina HiSeq 2000. Paired-end libraries with an average insert size of 180 bp were obtained. Raw reads were aligned to human genome 19 (hg19) using STAR aligner version 2.5.3.a [15]. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to evaluate RNA sequence quality. The RNA-seq data is available through the NCBI BioProject database (BLA: PRJNA551909, CE: PRJNA551908, NAC: PRJNA551775, SFC: PRJNA530758).