Year: 2024
Type: preprint
Abstract: Recent advances in single cell RNA sequencing, taxonomic classifications of cell types, and high resolution imaging of cell morphology has primed the field of neuroscience for new discoveries. Spatial transcriptomics has the potential to bridge these data modalities to each other by linking the molecular identity of cells to their native biological context. This protocol describes a method that utilizes expansion microscopy to perform multiple rounds of multiplexed fluorescent in situ hybridization (mFISH) on thick slices of brain tissue. It is adapted from EASI-FISH, where we have incorporated the more robust TREx gel chemistry to achieve better sample durability for ease of sample handling and extended rounds of probing. The protocol is optimized for retrospective FISH on fixed tissue using modalities such as optical physiology and tissue clearing/multiscale anatomy.
Authors: Rachel Flannery, Molly Logsdon, Laura Roy, Kevin Cao, Jayaram Chandrashekar
Institution: Allen Institute for Neural Dynamics
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4407684356