# High-throughput Single Cell Co-assay of Histone Modifications andTranscriptome

> **NIH NIH R44** · EPIGENOME TECHNOLOGIES, INC. · 2023 · $1,133,112

## Abstract

Summary
 Disruption of gene regulation is a major causal factor in heritable disease, developmental disorders,
and oncogenesis. While chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Tn5-
transposase based tagging (Cut&Tag) enable analysis of transcription factor binding and epigenetic state
profiling in bulk tissue samples and tumor biopsies, they produce only population average signals. Yet
regulatory networks and perturbations are heterogeneous between cell classes and types. Single-cell
technologies can overcome the challenge of cellular heterogeneity and provide deeper insight into cell
type-specific gene regulatory programs in healthy, diseased, and cancerous tissues. In prior work, we
developed a single-cell joint assay of histone modification and RNA expression (Paired-Tag), enabling
cell-type-stratified epigenetic profiling from bulk samples. This technology has attracted customers in
both academic and nonprofit research. In the proposed study, we will develop automated protocols and
effect laboratory informatics systems to establish a Paired-Tag services laboratory, we will refine our
protocol to improve experimental throughput and reduce cost, and we will develop a Paired-Tag “TF”
protocol for profiling transcription factor binding profiles. If successful, the research would enable next-
generation multi-omic analysis of tumor or disease samples at comparable cost to single-omic
technologies.

## Key facts

- **NIH application ID:** 10698374
- **Project number:** 2R44GM146330-02
- **Recipient organization:** EPIGENOME TECHNOLOGIES, INC.
- **Principal Investigator:** Christopher Hartl
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $1,133,112
- **Award type:** 2
- **Project period:** 2023-07-03 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10698374

## Citation

> US National Institutes of Health, RePORTER application 10698374, High-throughput Single Cell Co-assay of Histone Modifications andTranscriptome (2R44GM146330-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10698374. Licensed CC0.

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