RT Journal Article
SR Electronic
T1 A single-cell resolution gene expression atlas of the larval zebrafish brain
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.02.11.479024
DO 10.1101/2022.02.11.479024
A1 Inbal Shainer
A1 Enrico Kuehn
A1 Eva Laurell
A1 Mariam Al Kassar
A1 Nouwar Mokayes
A1 Shachar Sherman
A1 Johannes Larsch
A1 Michael Kunst
A1 Herwig Baier
YR 2022
UL http://biorxiv.org/content/early/2022/02/11/2022.02.11.479024.abstract
AB The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering in silico queries of cell types, connectivity and gene expression in regions of interest. We employed multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) to generate expression maps for an initial set of 200 marker genes across the larval zebrafish brain. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing co-visualization of gene expression patterns, single-neuron tracings, transgenic lines and anatomical segmentations. Additionally, brain activity maps of freely swimming larvae were generated at single-cell resolution using HCR labeling of the immediate-early gene cfos and integrated into the atlas. As a proof of concept, we identified a novel class of cerebellar eurydendroid cells that express calb2a, project to the hypothalamus and are activated in animals that have recently ingested food. Thus, a cellular-resolution gene expression atlas will not only help with rapid identification of marker genes for neuronal populations of interest, but also bridge the molecular and circuit levels by anchoring genetic information to functional activity maps and synaptic connectivity.Competing Interest StatementThe authors have declared no competing interest.