# PIPsceq: powering single cell RNA sequencing into the million cell era

> **NIH NIH R43** · FLUENT BIOSCIENCES INC. · 2020 · $399,059

## Abstract

Project Summary/Abstract
The dysregulation of multicellular regulatory networks is associated with nearly every human disease including
cancer, aging, autoimmunity and neurodegeneration. These networks of chemical, mechanical and electrical
signals allow cells organized within tissues to regulate collective decisions and behaviors. Our understanding
of the cell-cell interactions that underlie this dysregulation is hampered by a lack of tools to enable interrogation
of biological networks at the single cell level. In this Phase I SBIR, we will develop a generalized platform for
quantitative measurement of transcriptional changes of single cells at the massive scale required for highly
complex mechanistic studies of human disease. The routine availability of high-throughput tools for single-cell
RNA transcriptional analysis (scRNAseq), such as those based upon droplet microfluidics, has enabled new
mechanistic studies of cell types across tissues. These tools are based upon loading of individual cells into
water-in-oil droplets at limiting concentrations. However, these technologies have important limitations
prohibitive for highly complex mechanistic studies including lack of throughput necessary to efficiently analyze
hundreds of samples simultaneously or isolate >10,000 cells in a given reaction, high costs associated with
microfluidic devices and consumables, and problematic artifacts (e.g. doublets and batch effects). Recently,
scRNAseq sample multiplexing techniques have been described that introduce an oligonucleotide barcode to
mark all of the cells in a given sample such as the MULTI-seq approached developed by our collaborators Zev
Gartner and Eric Chow. We propose to expand the capability of Fluent BioSciences patented self-assembly
technology, Pre-templated Instant Partitions single cell expression quantitation (PIPsceq), for sample
multiplexing applications to enable high-complexity perturbational studies. PIPsceq is a controlled liquid
emulsification technology capable of instantaneous partitioning of millions of droplets without the use of
microfluidics representing up to 1000X increase in cell throughput per reaction over existing droplet
technologies. The sample multiplexing application (e.g. MULTI-seq) for PIPseq will form the basis of a
generalized platform for mechanistic studies of human disease by enabling paradigm-shifting increases in the
scale of digital droplet biology as well as reduce sample preparation costs and artifacts. Our overarching goal
is to develop prototype PIPsceq library preparation kits for sample multiplexing applications for > 100,000 cells
per reaction, which we believe will enable highly complex perturbational studies of individual cells that are not
feasible with existing technology. The aims of this Phase I SBIR are to demonstrate cell capture of an
unprecedented 10 million cells using PIPsceq and to produce prototype PIPsceq 100,000 cell library
preparation kits to be used for performance benchmarkin...

## Key facts

- **NIH application ID:** 10079618
- **Project number:** 1R43GM137648-01A1
- **Recipient organization:** FLUENT BIOSCIENCES INC.
- **Principal Investigator:** Kristina Fontanez
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $399,059
- **Award type:** 1
- **Project period:** 2020-08-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10079618

## Citation

> US National Institutes of Health, RePORTER application 10079618, PIPsceq: powering single cell RNA sequencing into the million cell era (1R43GM137648-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10079618. Licensed CC0.

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