bioRxiv preprint doi: https://doi.org/10.1101/2020.11.30.403865; this version posted December 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Transcriptome analysis for the development of cell-type specific labeling to study olfactory circuits Anzhelika Koldaeva1†, Cary Zhang1†, Yu-Pei Huang1†, Janine Reinert1, Seiya Mizuno2, Fumihiro Sugiyama2, Satoru Takahashi2, Taha Soliman1, Hiroaki Matsunami3, Izumi Fukunaga1* 1Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University 2Laboratory Animal Resource Center, Tsukuba University 3Department of Molecular Genetics and Microbiology and Department of Neurobiology, Duke University †These authors contributed equally. * To whom correspondence should be addressed (
[email protected]). Abstract In each sensory system of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioural repertoires. These often correspond to different cell types at some stage in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral and tufted cells (MCs and TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, little is known how these two types of projection neurons differ at the mRNA level. Here, we sought to identify genes that are differentially expressed between MCs and TCs, with an ultimate goal to generate a cell-type specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018).