# Generation of the Ci1 Reporter Mouse Strain with Enhanced Fluorescence for Tissue Clearing Applications

## TL;DR

Scientists created a new mouse strain with improved red fluorescence that works better with tissue clearing techniques used in neuroscience.

## Contribution

The Ci1 reporter mouse strain offers enhanced fluorescence and reduced leakage for tissue clearing applications.

## Key findings

- The Ci1 reporter strain shows stronger fluorescence intensity in various tissues compared to Ai14.
- Fluorescence is better preserved after tissue clearing in Ci1 mice.
- The Ci1 strain has minimal non-specific leakage across organs and tissue types.

## Abstract

The advancement of tissue clearing technology has significantly propelled neuroscience research. Nevertheless, the fluorescent proteins used in traditional transgenic mouse strains were not specifically optimized for tissue clearing procedures, resulting in a substantial decrease in fluorescent intensity after clearing. In this study, we developed the Ci1 reporter mouse strain (where Ci stands for the Chinese Institute for Brain Research, CIBR) based on the bright red fluorescent protein mScarlet. The Ci1 reporter exhibits no fluorescence leakage in various organs or tissue types and can be readily crossed with multiple tissue-specific Cre lines. Compared to the Ai14 mouse strain, the Ci1 reporter strain demonstrates lower non-specific leakage, stronger fluorescence intensity in different tissues, and better preservation of fluorescence following tissue clearing treatment. The creation of the Ci1 reporter provides a more effective tool for both neuroscience and other biomedical research applications.

The online version contains supplementary material available at 10.1007/s12264-025-01421-4.