Ventral tegmental area brain region from wild-type and Clock delta 19 mutant mice in response to valproate or ACY957 compound

We report the gene expression changes in the ventral tegmental area brain region from wild-type and Clock delta 19 mutant mice in response to valproate or ACY957 compound. RNA was extracted from these regions then processed for RNAseq. Brains were extracted and flash frozen from adult male ClockΔ19 or Wildtype mice treated with valproate (VPA), ACY957, or their respective vehicles for 14 days (See above). Tissue was collected at ZT6, approximately 24 hrs after the last treatment. Multiple bilateral 1mm punches were taken centered over the ventral tegmental area (VTA). Individual mice were used as biological replicates (8 mice x 2 genotypes x 4 treatments = 64 samples). Mouse brain tissue punches were homogenized and total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively. Libraries were prepared using TruSeq Stranded mRNA (PolyA+) kit (Illumina, San Diego, CA) and sequenced by Illumina NextSeq 500. The read length was 75bp with 30-40M reads per sample. FastQC (v0.11.3) was performed to assess data quality. TopHat2 (v2.0.9) aligned the reads to the mouse reference genome (Mus musculus UCSC mm10) and to the Ensembl human reference genome (GRCh38.p13) using default parameters. Alignments were then converted to expression count data using HTseq (v0.6.1) with default union mode. The RNAseq count data were transformed to log2 count data using voom function of the Bioconductor limma package..