# Spatially Resolved Transcriptomics Enabled by Ultrabright Pdot Probes for Interrogation of Complex Tissues

> **NIH NIH R01** · UNIVERSITY OF WASHINGTON · 2020 · $689,482

## Abstract

Abstract
We propose to develop a transformative approach to measure gene expression in situ in complex
tissues based on three innovations. First, we will develop a large palette spectrally-barcoded
fluorescent polymer-dot (Pdot) probes which will be used to label mRNA within an intact tissue; the
unique spectral signatures of the Pdots allow the identification of up to thousands of distinct mRNA
molecules as a readout of gene expression. Second, we propose to develop improved materials to clear
and expand tissues based on swellable polymer hydrogels. These improved materials will lower mRNA
concentrations so that many can be read out at one time without spatially overlapping. Third, we
propose to develop a new light sheet microscope which is able to rapidly interrogate tissue volumes and
read out the spectral barcodes on the individual Pdot probes. We will use these tools together to study
brain development of the mouse visual cortex, a model system for the mammalian brain. Our
methodology should also be widely applicable to the study of other complex tissues and or small
organisms.

## Key facts

- **NIH application ID:** 9929636
- **Project number:** 5R01MH115767-04
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Daniel T Chiu
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $689,482
- **Award type:** 5
- **Project period:** 2017-09-01 → 2022-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9929636

## Citation

> US National Institutes of Health, RePORTER application 9929636, Spatially Resolved Transcriptomics Enabled by Ultrabright Pdot Probes for Interrogation of Complex Tissues (5R01MH115767-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9929636. Licensed CC0.

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