# Developing Antibody-Oligonucleotide Bridges to Simplify Single Cell Spatial Transcriptomics

> **NIH NIH R21** · REGENERATIVE RESEARCH FOUNDATION · 2022 · $261,000

## Abstract

Project Summary
 Single cell RNA-sequencing (scRNA-seq) has enabled researchers to investigate a wide array of
biological processes and how tissue heterogeneity contributes to function. These technologies have led to the
development of programs, such as the NIH Human Biomolecular Atlas Program, to understand how cells
interact in an organism to drive its function. The development of spatial transcriptomic technologies has
allowed researchers to investigate how cell-cell interactions affect cellular gene expression within a tissue.
Current approaches generally rely in situ RNA based methodolgies or slide-based sequencing in combination
with scRNA-seq (e.g. Slide-seq) to generate spatial maps of interacting cells. These technologies have helped
demonstrate the power of combining the tissues structural data with transcriptional data to better understand
cell behavior in a tissue and going forward improving the interface between these technologies will be key to
uncovering how structure and cell transcription drives function. However, multiple barriers impede the
widespread adoption of the current methods for performing spatial transcriptomics, including significant
financial cost, time requirements, and a lack of sufficient expertise. Herein, we propose to develop a simple
reagent compatible with current protocols for drop-based and pipette-based scRNA-seq technologies. This
reagent will be able to generate spatial data in the normal course of scRNA-seq experiments without
significantly increasing cost or time commitments. We propose to invent “antibody-oligonucleotide bridges” and
build software capable of bioinformatically generating a network of cell-cell contacts across the tissue to
recapitulate the spatial relationships of the cells in a tissue. In this proposal, we will carry out a proof-of-
principal experiment for the AO bridge scRNA-seq approach for generating the spatial relationships between
cells.

## Key facts

- **NIH application ID:** 10372550
- **Project number:** 1R21GM140328-01A1
- **Recipient organization:** REGENERATIVE RESEARCH FOUNDATION
- **Principal Investigator:** Nathan C Boles
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $261,000
- **Award type:** 1
- **Project period:** 2022-03-01 → 2024-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10372550

## Citation

> US National Institutes of Health, RePORTER application 10372550, Developing Antibody-Oligonucleotide Bridges to Simplify Single Cell Spatial Transcriptomics (1R21GM140328-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10372550. Licensed CC0.

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