Single-Cell Transcriptomes and Whole-Brain Projections of Serotonin Neurons in the Mouse Dorsal and Median Raphe Nuclei

We performed a comprehensive survey of DR and MR serotonin neurons in the adult mouse brain by scRNA-seq. To specifically label serotonin neurons, we crossed Sert-Cre mice (Gong et al., 2007) with the tdTomato Cre reporter mouse, Ai14 (Madisen et al., 2010). (Serotonin transporter, or Sert, is a marker for serotonin neurons; see more details below.) We collected serotonin neurons acutely dissociated from brain slices by fluorescence-activated cell sorting (FACS) and used Smart-seq2 (Picelli et al., 2013) to generate scRNA-seq libraries. We used both male and female adult mice (postnatal day 40-45) and applied two dissection strategies to separate the serotonin neurons originating from anatomically-distinct brain regions: 1) in the first set of experiments, we dissected the brainstem region that contain the entire MR and DR; 2) in the second set of experiments, we focused on the principal DR (pDR, corresponding to the traditional B7 group) region by dissecting specifically the DR but excluding its caudal extension (cDR, corresponding to the traditional group B6). After quality control, we determined the transcriptomes of 709 cells from eight samples that include MR, pDR, and cDR, and 290 cells from six pDR-only samples (999 cells passing quality threshold out of 1536 total cells). We sequenced to a depth of ~1 million reads per cell and detected ~10,000 genes per cell.