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1 Janelia Publications

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    03/08/21 | Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization
    Yuhan Wang , Mark Eddison , Greg Fleishman , Martin Weigert , Shengjin Xu , Frederick E. Henry , Tim Wang , Andrew L. Lemire , Uwe Schmidt , Hui Yang , Konrad Rokicki , Cristian Goina , Karel Svoboda , Eugene W. Myers , Stephan Saalfeld , Wyatt Korff , Scott M. Sternson , Paul W. Tillberg
    bioRxiv. 2021 Mar 8:. doi: 10.1101/2021.03.08.434304

    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 novel spatially and molecularly defined subregions. EASI-FISH also facilitates iterative re-analysis 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.

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