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The transcriptome sequencing data of valproic acid (VPA) model of autism and control rats are presented. VPA model of autism was induced by a single intraperitoneal injection of 600 mg/kg sodium valproic acid to female rats at day 12.5 post-conception, and the control rats were injected with saline. Male offspring of VPA- or saline-injected dams from different litters were sacrificed on PND 35 (n = three rats/three litters/group). Prefrontal cortex was dissected from both hemispheres, and RNA was isolated. Libraries were prepared and RNA Sequencing (RNA-Seq) was performed following Illumina's recommendations. Samples are described in the SRA portal (SRP115258) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRR5950172 to SRR5950177). The interpretation of these data is presented in the following research article: “Transcriptional and splicing dysregulation in prefrontal cortex of valproic acid induced rat models of autism” (Zhang et al., 2018) [1].