# OPTICAL, FLUIDIC, AND MOLECULAR TECHNOLOGIES FOR SINGLE-CELL OMICS

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA BERKELEY · 2021 · $381,139

## Abstract

SUMMARY
Stem cell differentiation takes place on a complex landscape defined by a continuum of intermediate cell states,
branching trajectories, and highly coordinated regulatory dynamics. This complexity is often hidden to
ensemble measurements, which are typically limited to measuring average values of markers in populations of
cells. The recent and rapid emergence of high-throughput single-cell RNA sequencing has provided a powerful
solution for dissecting transitions between cell states by measuring the expression of thousands of genes in
large populations of cells. Complementary statistical tools can process these large data sets and identify
distinct groups of cells base on their transcriptional profile. However, RNA transcript abundance does not
always correlate with protein composition and there are many important intracellular molecules, like lipids and
metabolites, which are not specifically encoded in the genome. Orthogonal molecular measurements of cell
state could provide a powerful complement to transcriptome analysis for investigating regulatory dynamics
during stem cell differentiation. This research program focuses on the development of technology to facilitate
“multi-omic” measurements in single cells. We take advantage of three core technologies to measure cell state
phenotypes. We use DamID to probe genome organization and protein-DNA interactions, single-cell RNAseq
to provide whole-transcriptome gene expression profiling, and coherent Raman imaging to characterize the
chemical composition of live cells. Microfluidic technology facilitates the integration of these techniques and
enables multimodal measurement of single cells. This platform will provide a new approach for dissecting
coordinated regulatory networks in differentiating stem cells. Our ultimate goal is to develop a tool to make all
of these measurements in situ, in order to retain single-cell spatial information and cellular context in a
developing tissue or whole organism.

## Key facts

- **NIH application ID:** 10242149
- **Project number:** 5R35GM124916-05
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Aaron Streets
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $381,139
- **Award type:** 5
- **Project period:** 2017-08-01 → 2024-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10242149

## Citation

> US National Institutes of Health, RePORTER application 10242149, OPTICAL, FLUIDIC, AND MOLECULAR TECHNOLOGIES FOR SINGLE-CELL OMICS (5R35GM124916-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10242149. Licensed CC0.

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