# Optimizing MERFISH to allow multiplexed measurement of developmental and tonotopicgene expression gradients in the cochlea

> **NIH NIH R21** · BAYLOR COLLEGE OF MEDICINE · 2024 · $200,000

## Abstract

PROJECT SUMMARY
 The adult cochlea presents many technical hurdles to researchers studying the normal function of its
constituent cell types, and how these cell types respond to injury, aging and degeneration. Because the
cochlea is encased in strong bone and contains relatively small numbers of cells compared to other sensory
organs such as the retina, isolating cells to characterize their structure, physiology or gene expression is
challenging. Moreover, histological methods to make the cochlea more accessible, such as decalcification, are
harsh treatments that can degrade mRNA or protein. In this pilot R21 proposal, we will assess the feasibility of
a recently-developed technique known as MERFISH – Multiplexed Error-Robust Fluorescence In Situ
Hybridization – to simultaneously detect and quantify the expression of hundreds of genes in the cochlea. We
believe this technique is sensitive enough to reveal quantitative differences in gene expression along the
developmental and tonotopic gradients that exist along the basal-apical axis of the cochlea. Developing a
robust protocol to detect, quantify and spatially localize hundreds of genes at once has the ability to transform
our understanding of the normal function of the cochlea, and how gene expression changes in the cochlea and
spiral ganglion after noise exposure, hair cell loss, aging and drug administration. The goal of this proposal is
to demonstrate the feasibility of MERFISH in the neonatal and adult cochlea and to develop protocols to allow
MERFISH to be used by the hearing and balance community.

## Key facts

- **NIH application ID:** 10795676
- **Project number:** 5R21DC021041-02
- **Recipient organization:** BAYLOR COLLEGE OF MEDICINE
- **Principal Investigator:** Andrew K Groves
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $200,000
- **Award type:** 5
- **Project period:** 2023-04-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10795676

## Citation

> US National Institutes of Health, RePORTER application 10795676, Optimizing MERFISH to allow multiplexed measurement of developmental and tonotopicgene expression gradients in the cochlea (5R21DC021041-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10795676. Licensed CC0.

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