# Deployable, Single-use Device for Single Cell Genomics in Clinical Research

> **NIH NIH R44** · HONEYCOMB BIOTECHNOLOGIES, INC. · 2022 · $656,166

## Abstract

Project Summary
Single cell RNA-seq (scRNA-seq) has emerged as a potent tool for delineating cell states in
heterogeneous cell populations. However, leveraging this potent technology in clinical research and
care is challenging due to the logistics of stabilizing the transcriptional profiles soon after sample
collection. We have demonstrated feasibility of a single use cassette that integrates sample collection,
storage and processing of clinical samples to scRNA-seq libraries. The cassette leverages a picoliter-well
array pre-loaded with barcoded transcript capture beads to collect and isolate single cells. A cell
preservation reagent is added to the cassette to stabilize the transcript profiles in their native state. An
elastomeric plunger is used to seal the array with a semipermeable membrane using a simple snapping
mechanism. The sealed cassette can be sent to a central facility for batch processing to sequencing
libraries. No specialized equipment is required for collection and storing cells at clinical sites, enabling
facile deployment of the technology to multiple clinical sites. We propose to finish development and
validate the manufacturing and user workflows for the cassette. Specifically we will 1) harden the
manufacturing protocols for generating the cassettes and perform a multi-lot validation campaign, 2)
develop and validate a simple workflow for processing and loading clinical samples into the cassette and
3) validate central processing of samples collected and stored in the cassettes by distributed labs. To
achieve these goals, we have created a strong consortium including the core Honeycomb team, advisors
Dr. Alex Shalek and Dr. Christopher Love, two experts in single cell analysis and co-developers of the
underlying technology, and two large pharma partners who have significant experience in the
requirements for clinical research and will be extensively validating the technology.

## Key facts

- **NIH application ID:** 10457403
- **Project number:** 5R44HG011605-02
- **Recipient organization:** HONEYCOMB BIOTECHNOLOGIES, INC.
- **Principal Investigator:** Todd M Gierahn
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $656,166
- **Award type:** 5
- **Project period:** 2021-08-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10457403

## Citation

> US National Institutes of Health, RePORTER application 10457403, Deployable, Single-use Device for Single Cell Genomics in Clinical Research (5R44HG011605-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10457403. Licensed CC0.

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