A single-cell resolution gene expression atlas of the larval zebrafish brain

• DOI: 10.1101/2022.02.11.479024
• Publication Date: 2022-02-12T04:30:37Z
• Authors: Inbal Shainer; Enrico Kuehn; Eva Laurell; Mariam Al Kassar; Nouwar Mokayes; Shachar Sherman; Johannes Larsch; Michael Kunst; Herwig Baier
• Keywords: Brain atlas

Abstract The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering silico queries cell types, connectivity and gene expression regions interest. We employed multiplexed fluorescent situ RNA hybridization chain reaction (HCR) generate maps for an initial set 200 marker genes across the larval zebrafish brain. data were registered Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing co-visualization patterns, single-neuron tracings, transgenic lines anatomical segmentations. Additionally, activity freely swimming larvae generated at single-cell resolution using HCR labeling immediate-early cfos integrated into atlas. As a proof concept, we identified novel class cerebellar eurydendroid cells that express calb2a , project hypothalamus are activated animals have recently ingested food. Thus, cellular-resolution atlas will not only help with rapid identification neuronal populations interest, but also bridge molecular circuit levels anchoring genetic information functional synaptic connectivity.