# In situ Single-Cell Multi-Omic and Morphological Profiling in Mammalian Brains

> **NIH NIH RF1** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2022 · $1,809,488

## Abstract

PROJECT SUMMARY
Single-cell technologies have revolutionized the characterization of mammalian brains allowing unbiased census
of cell types and their transcriptomic and epigenomics signatures. However, the mapping of molecular signatures
onto three-dimensional brain structures remains highly challenging since most single-cell methods can only
analyze disassociated cells or nuclei. We propose to develop photonic-indexing sequencing (pi-seq) strategies
for in situ spatial barcoding with single-cell resolution. The proposed pi-seq strategy writes high complexity
molecular barcodes into the tissue using sequential ligation of DNA indices with the ligation reaction controlled
by high-resolution patterned illumination. Chromatin accessibility and cytosine modifications are well-established
epigenomics marks playing critical roles in transcription regulation in normal and disease tissues. We will
integrate pi-seq with existing single-cell epigenomics techniques to develop methods for the spatial profiling of
chromatin accessibility (pi-ATAC-seq) and methylcytosine (pi-mC-seq). We will further develop an in situ method
pi-mCAT-seq to simultaneously profile RNA, methylcytosine, and chromatin accessibility at a single-cell
resolution based upon our single-nucleus multi-omics method snmC2T-seq. The spatial specificity and data
quality of pi-seq methods will be systematically evaluated using single-cell epigenomic datasets generated by
BICCN. To connect molecular profiles with other defining properties of brain cell types such as morphology and
synaptic connectivity, we will develop methods to integrate pi-seq with MORF (Mosaicism with Repeat
Frameshift), a sparse and genetic labeling approach of neurons and glia to illuminate their complete
morphologies (dendrites, axons, synapses). The proposed pi-seq methods will provide the tools to construct
spatially resolved epigenomic atlas of mammalian brains and advance the study of gene regulation in brain
development, function, and disease at the resolution of single cells.

## Key facts

- **NIH application ID:** 10506297
- **Project number:** 1RF1MH130461-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** Chongyuan Luo
- **Activity code:** RF1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $1,809,488
- **Award type:** 1
- **Project period:** 2022-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10506297

## Citation

> US National Institutes of Health, RePORTER application 10506297, In situ Single-Cell Multi-Omic and Morphological Profiling in Mammalian Brains (1RF1MH130461-01). Retrieved via AI Analytics 2026-05-29 from https://api.ai-analytics.org/grant/nih/10506297. Licensed CC0.

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