Single nucleus RNA-seq of prefrontal cortex from methamphetamine-treated mice and control mice

As one of the most commonly abused substances in the world, methamphetamine (METH) addiction and use disorders cause a huge burden for society. The prefrontal cortex (PFC) is a vital brain region associated with emotion and cognitive behaviors that is also intimately involved in the neurocircuitry of addiction syndrome. Bulk RNA-seq has revealed the effects of METH on disease-related genes alterations in the mouse PFC; however, the roles of different cell types are still unknown. We performed single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of 20,698 nuclei isolated from the PFC of chronic METH-treated and control mice. Animals included in current study were all 2-month-old male C57BL/6 mice. All animals were socially housed on a 12-h light/dark cycle with water and food ad libitum. Mice were treated with 5 mg/kg METH or saline (intraperitoneal) for 14 days in the METH and control groups, respectively. Then all mice were deeply anesthetized with chloral hydrate and sacrificed, and the PFCs of three mice per group were rapidly removed and prepared for single nucleus isolation on ice. Then Iodixanol gradient centrifugation was used for single nucleus isolation. The library sequencing was performed in the Illumina Hiseq platform (Illumina, San Diego, CA, USA) under the 2 × 150-bp double-ended sequencing pattern to generate FastQ data.