# Development of CLADE: Cell Lineage Annotating DNA Elements

> **NIH NIH R21** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2020 · $192,076

## Abstract

ABSTRACT
The relatively recent development of droplet-based single cell RNA sequencing (scRNA-seq)
techniques has changed the landscape of several fields of research. It has enabled
investigators to elucidate the cellular complexities in tissues, organs, and tumors which have
traditionally been treated as homogeneous. The new perspective is important for understanding
the biology underlying normal and disease conditions, and it will stimulate development of new
therapies that take advantage of the more granular understanding of physiological systems.
With this new perspective comes a realization of some of the limits to scRNA-seq, and barriers
that must be overcome to achieve potential of single cell analyses. This proposal focuses on
developing an innovative new technology that will dramatically improve the impact of scRNA-
seq techniques applied to stem cell research and regenerative medicine therapies. Currently,
scRNA-seq is great at identifying the cellular components within a sample, but it is incapable of
discerning the route individual cells took through a cell lineage. It is critical to determine cell
lineages because they provide the essential instructions informing protocols for directed
differentiation and cell based therapies. The proposal's system, named Cell Lineage Annotating
DNA Elements (CLADE) will introduce into stem cells a library of individually barcoded plasmid
DNAs. Using elements of episomal DNA maintenance system from the Epstein-Barr virus, the
CLADE plasmid barcode will change as cells undergo cell divisions, resulting in a unique cohort
of barcoded plasmids for individual cells. By using the same reaction to generate scRNA-seq
transcriptomes and CLADE identification, the system will provide a seamless way of
determining ancestry of cells alongside their transcriptomic identity. Through a series of six
Milestones, the CLADE system will be synthesized, tested, and developed so that it can be
readily used by other groups using scRNA-seq and stem cells. We anticipate CLADE will enable
a near comprehensive cellular ancestry to be determined for >40,000 individual cells for >10
generations of cell division. Compared to current capabilities of hundreds of cells and two or
three cell divisions, CLADE can massively increase capacity for identifying cell lineages and
have a long lasting impact on fields that benefit from scRNA-seq research.

## Key facts

- **NIH application ID:** 9922394
- **Project number:** 5R21OD027080-02
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** Bradley J Merrill
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $192,076
- **Award type:** 5
- **Project period:** 2019-05-01 → 2022-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9922394

## Citation

> US National Institutes of Health, RePORTER application 9922394, Development of CLADE: Cell Lineage Annotating DNA Elements (5R21OD027080-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/9922394. Licensed CC0.

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