# PARALLEL ANALYSIS OF TRANSCRIPTION AND PROTEIN-DNAINTERACTIONS IN SINGLE CNS CELLS

> **NIH NIH RF1** · WASHINGTON UNIVERSITY · 2020 · $93,247

## Abstract

PROJECT SUMMARY
The brain is the most complex organ in the body, consisting of hundreds of molecularly, physiologically, and
anatomically distinct cells. Recently, methods have been developed that can cost-effectively measure mRNA
abundance in tens of thousands of single cells, and this has led to a revolution in the identification and
classification of new types of cells in the brain. But these methods only measure one aspect of gene regulation
– mRNA levels. To fully understand the transcriptional networks that function in the brain, it will be important to
also map the genome-wide binding locations of transcription factors and chromatin modifiers in the myriad of
different cell types present in the brain. We propose to develop a method to simultaneously map transcription
factor binding and measure mRNA abundance from single cells in the brain. To do so, we will adapt our
transposon based methods for measuring the binding of DNA interacting proteins to existing single cell profiling
methods. This technology, single-cell Calling Cards, builds on our previously developed transposon Calling Card
method, but significantly extends the method allowing use in populations of heterogeneous cells, without a priori
definition of cell type. We propose here to develop new mouse lines compatible with the wide range of existing
resources in mouse, as well as viral and plasmid reagents applicable across model species, and distribute these
to the community. Finally, since the tools we will develop generate new types of data, we will develop a user-
friendly software for data visualization and analysis of TFs or chromatin modifying proteins binding data across
multiple cell types. Robust resources for analysis are crucial if these technologies are to find broad use in the
community. Our primary goal is to enable the parallel analysis of transcription factor binding and mRNA
expression levels from tens of thousands of single cells in the brain.
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## Key facts

- **NIH application ID:** 10044139
- **Project number:** 3RF1MH117070-01S1
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** JOSEPH D DOUGHERTY
- **Activity code:** RF1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $93,247
- **Award type:** 3
- **Project period:** 2020-01-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10044139

## Citation

> US National Institutes of Health, RePORTER application 10044139, PARALLEL ANALYSIS OF TRANSCRIPTION AND PROTEIN-DNAINTERACTIONS IN SINGLE CNS CELLS (3RF1MH117070-01S1). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10044139. Licensed CC0.

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