1. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization
- Author
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Yuhan Wang, Mark Eddison, Greg Fleishman, Martin Weigert, Shengjin Xu, Tim Wang, Konrad Rokicki, Cristian Goina, Fredrick E. Henry, Andrew L. Lemire, Uwe Schmidt, Hui Yang, Karel Svoboda, Eugene W. Myers, Stephan Saalfeld, Wyatt Korff, Scott M. Sternson, and Paul W. Tillberg
- Subjects
Male ,projections ,Transcription, Genetic ,Gene Expression Profiling ,Neuropeptides ,neurons ,area ,populations ,General Biochemistry, Genetics and Molecular Biology ,Mice, Inbred C57BL ,Imaging, Three-Dimensional ,Gene Expression Regulation ,parallel ,single cells ,Hypothalamic Area, Lateral ,expression ,Animals ,rna ,rat ,RNA-Seq ,Single-Cell Analysis ,Proto-Oncogene Proteins c-fos ,Biomarkers ,In Situ Hybridization, Fluorescence ,mouse - Abstract
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.