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EASI-FISH enabled spatial analysis of molecular cell types in the lateral hypothalamus

posted on 05.03.2021, 02:59 by Yuhan Wang, Mark Eddison, Greg Fleishman, Martin Weigert, Shengjin Xu, Fredrick E. Henry, Tim Wang, Andrew Lemire, Uwe Schmidt, Hui Yang, Konrad Rokicki, Cristian Goina, Karel Svoboda, Eugene W Myers, Stephan Saalfeld, Wyatt Korff, Scott M. Sternson, Paul W. Tillberg

Expansion-Assisted Iterative Fluorescence in situ hybridization (EASI-FISH) allows spatial analysis of molecular cell types in thick tissue volumes (300µm). We applied EASI-FISH to the mouse lateral hypothalamus (LHA), a brain region that has been studied for decades as an important motivational center regulating ingestive, social, arousal, and autonomic functions. Despite extensive functional investigation, the understanding of the LHA is limited by poor anatomical definition. Here, we performed EASI-FISH using 24 molecular cell type markers identified from scRNA-Seq and uncovered an unexpected parcellation of the LHA not previously described from cell density measurements. It also reveals morphological diversity of neuronal types in this region.

'EASI_FISH_gene_count.csv' contains spot count per cell for all marker genes probed. Marker genes, Meis2 and Th were probed twice (R1 and R9) to evaluate the RNA stability of the samples. Columns are marker genes and rows are neuron IDs. Data collected from three animals (LHA1, LHA2 and LHA3).

'EASI_FISH_metadata.csv' contains metadata for each neuron. Rows are neuron IDs and columns are metadata, including neuronal position (z, y, x, after rigid alignment), soma volume (area), soma shape (aspect ratio and solidity), molecular cell type it belongs to (cell type), etc. All measurements presented here in pre-expansion units.


HHMI Janelia Research Campus




Janelia Research Campus