Transcriptional profiling of mammalian habenula using scRNAseq

The habenula complex is appreciated as a critical regulator of motivated and pathological behavioral states via its output to midbrain nuclei. Despite this, transcriptional definition of cell populations that comprise both the medial (MHb) and lateral habenular (LHb) subregions in mammals remain undefined. To resolve this, we performed single-cell transcriptional profiling and highly multiplexed in situ hybridization experiments of the mouse habenula complex in naïve mice and those exposed to an acute aversive stimulus. Transcriptionally distinct neuronal cell types identified within the MHb and LHb, were spatially defined, and differentially engaged by aversive stimuli. Cell types identified in mice, also displayed a high degree of transcriptional similarity to those previously described in zebrafish, highlighting the well conserved nature of habenular cell types across the phylum. These data identify key molecular targets within habenula cell types, and provide a critical resource for future studies. We applied scRNAseq to unbiasedly characterize mammalian habenula transcriptome. We obtained transcriptional dataset of 11,878 cells including 5,558 neuronal cells. To characterize transcriptional identities of single cells in the mammalian habenula, we utilized droplet based chromium technology developed by 10x Genomics. We microdissected the habenula from brain live slices of adult male mice (P50-55), enzymatically digested the tissue to obtain well dissociated highly viable single cells (viability >80 %), captured single cell transcriptomes, and generated cDNA libraries for subsequent sequencing.