# Gel-based Optical-isolation Single-Cell 3D Spatial Multiomics

> **NIH NIH DP2** · UNIVERSITY OF CALIFORNIA-IRVINE · 2022 · $1,378,306

## Abstract

ABSTRACT
 Proper functioning of the human body relies on the organization of cells in 3D space. A cell’s function
and fate are determined by its biomolecule composition and its 3D environment. The spatially identification of
proteins, RNAs, and DNAs in a tissue thus provides a powerful map to decipher how cells build tissues and
become diseased. Through the use of single-cell omics, it’s been possible to reveal rare cell types that
benchmark development, oncogenesis, and brain functions. However, the cell isolation process in single-cell
analysis unavoidably causes loss of spatial information. To obtain spatial information, spatial transcriptomics
based on imaging or sequencing have emerged to give insight into the heterogeneous expression patterns in
tumors, brain, and wound tissues. Unfortunately, most spatial transcriptomics methods can only examine thin
tissue sections, and are incompatible with proteomics. To address these drawbacks, the goal of the project is to
develop a conceptually novel 3D spatial multiomics technology featuring gel-based optical isolation (GO3D). The
proposed GO3D technology is distinct from all current spatial omics, and will enable the profiling of proteins,
RNAs, and DNAs of whole-mount tissues with subcellular resolution, high coverage and high throughput,
simultaneously. This innovative design is based on the gel-based label-retention expansion microscopy (LR-
ExM) that the PI published recently. GO3D will drastically transform our understanding of many critical biomedical
questions, which we lack of tools to address currently. For example, how are cells in a highly dynamic skin
migrate in 3D to heal wounds? How do specialized neurons build brain? And where do microbes interact with
what cell types in gut?

## Key facts

- **NIH application ID:** 10473394
- **Project number:** 1DP2GM150017-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** Xiaoyu Shi
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,378,306
- **Award type:** 1
- **Project period:** 2022-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10473394

## Citation

> US National Institutes of Health, RePORTER application 10473394, Gel-based Optical-isolation Single-Cell 3D Spatial Multiomics (1DP2GM150017-01). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10473394. Licensed CC0.

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