# A transposase system for integrative ChIP-exo and ATAC-seq analysis at single-cell resolution

> **NIH NIH R01** · STOWERS INSTITUTE FOR MEDICAL RESEARCH · 2020 · $527,588

## Abstract

PROJECT SUMMARY
Predicting cis-regulatory information from sequence alone is not yet possible, but collecting cis-regulatory
information systematically across all human cell types and across species would be feasible with significant
progress in technology. Here we propose to develop such breakthrough technology that will allow to extract
cis-regulatory information from any cell type, including mixtures of heterogeneous cell types. The technology is
based on a transposase system that combines ChIP and ATAC-seq technology, and thus allows the
simultaneous measurement of chromatin accessibility and transcription factor occupancy in the same cells. It is
innovative in its orders of magnitude improvement in efficiency by which DNA fragments enter the genomic
library, which allows the assay to be performed at single-cell resolution. It is cutting-edge in its resolution,
which allows the identification of precise footprints of transcription factor bound in vivo. We will optimize scale
and workflow, as well as develop an initial analysis framework, to make the technology applicable to a wide
range of systems. As proof-of-principle, we will apply the technology to early mouse embryos and compare the
results to those obtained from mouse embryonic stem cells. Having such technology will open the door to
unprecedented explorations of cis-regulatory information across any cell type. It will deepen our understanding
of transcriptional regulatory networks during development and evolution, and will provide insights into
mutations and mechanisms underlying human disease.

## Key facts

- **NIH application ID:** 9948716
- **Project number:** 5R01HG010211-03
- **Recipient organization:** STOWERS INSTITUTE FOR MEDICAL RESEARCH
- **Principal Investigator:** Julia Zeitlinger
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $527,588
- **Award type:** 5
- **Project period:** 2018-09-14 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9948716

## Citation

> US National Institutes of Health, RePORTER application 9948716, A transposase system for integrative ChIP-exo and ATAC-seq analysis at single-cell resolution (5R01HG010211-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9948716. Licensed CC0.

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