Max Planck Team Builds Single-Cell Gene Expression Atlas for Larval Zebrafish Brain

A gene expression atlas of the larval zebrafish brain at single-cell resolution is presented in Science Advances this week, representing a new tool for investigating neuronal circuit development and structure in a widely used vertebrate model. Aiming to expand upon the various neuroscience resources for larval zebrafish, a team of Max Planck Institute for Biological Intelligence scientists used multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) technology to generate whole-brain, single-cell resolution gene expression maps for a set of 290 marker genes, coregistered with thousands of single-neuron tracings, hundreds of transgenic lines, and more than 120 expertly curated anatomical segmentations in the Max Planck Zebrafish Brain atlas, dubbed Mapzebrain. The researchers also report a novel HCR FISH protocol for detecting RNA of the immediate early response gene cfos following various sensory stimulations and behavioral tasks. The atlas data is freely available through the Mapzebrain website. "This new resource, which can be straightforwardly expanded in the future by community contributions, offers convenient web-based access to markers of neuronal subpopulations," they write.