HIVE scRNAseq Solution

Expand the Possibilities for Single Cell Transcriptional Profiling

Biological resolution at the level of individual cells is powering the next phase of precision health. Developed by Honeycomb Biotechnologies, the HIVE™ scRNAseq Solution integrates sample storage and single cell profiling into a complete workflow, solving the issues that limit single cell RNA analysis by:

  • Enabling multi-site and multi-timepoint sample collection

  • Maintaining sample integrity through storage, shipping, and processing

  • Increasing the recovery rates of fragile cells

  • Facilitating loading of larger sample volumes

  • Delivering flexible and scalable workflows by enabling batch processing

  • Removing the need for specialized instrumentation

The HIVE™ Device is a portable, handheld, single-use device that enables gentle capture, robust storage, and easy processing for the analysis of single-cell samples. The HIVE™ scRNAseq Solution will expand single-cell analysis in basic, translational, pre-clinical, and clinical research applications.

Visit Honeycomb’s Website to access HIVE scRNAseq™ protocols and technical information.

Expand your possibilities with enhanced single cell transcriptional profiling
For research use only. Not for use in diagnostic procedures.
HIVE™ scRNAseq Solution


HIVE scRNAseq Solution Workflow

Enabling Multi-site & Multi-timepoint Sample Collection

The HIVE™ scRNAseq solution is a combined sample storage and single-cell profiling system. The HIVE™ device delivers versatility by enabling sample collection at different sites or at different timepoints and sample processing at the same location where they are collected or at a centralized processing laboratory.

Easy to Use

The HIVE™ scRNAseq solution incorporates reagents and a single-use, handheld, shippable HIVE™ device that can be used in almost any lab environment. No specialized equipment is required to process the samples from single cells through library preparation and the workflow can be run in most labs.

A clinical researcher receives bone marrow biopsies at odd hours, making it challenging to process them fresh and at the same time for ideal data quality. Additionally, the specialized equipment required for her current single cell solution is not always available. With the HIVE™ device, she can capture her samples at any time, then store her cell-loaded HIVE™ device(s) until all samples are ready for processing together, as if they had been processed fresh.

With a sample storage solution built into the capture and processing workflows, the HIVE™ devices provide a stable environment to arrest cells in their current states and protect the sample over time.

Maintaining Sample Integrity

Cell quality is not compromised when using the HIVE™ device during storage, shipping or processing. As can be seen in Figure 1, single cell libraries prepared from fresh cells and cells stored at -20°C for 14 days prior to processing have similar profiles, showing no loss of cell population diversity, number of transcripts or genes detected.

Figure 1. Comparison between samples processed while fresh or stored at -20°C for 14 days prior to processing.
Maintaining Sample Integrity

A researcher has been attempting to recover neutrophils from whole blood samples. He has been struggling to recover neutrophils with current microfluidic platforms in the lab, but the HIVE™ device’s gentle capture of cells enables him to generate data for neutrophils and other fragile cell types.

The HIVE™ scRNAseq solution delivers comprehensive biological representation,
including fragile and sparse cells.

Increasing the Recovery Rates of Fragile Cells

Increasing the Recovery Rates of Fragile Cells

Cells isolated using the HIVE™ device settle gently into microwells within a matter of minutes. This change enables the analysis of cells that are typically difficult to analyze either because of their fragile membrane structures or because they have been stimulated or transfected which can induce fragility. Figure 2 shows the HIVE™ scRNAseq workflow is able to recover granulocytes which are difficult to detect with other platforms because of their fragility.

Figure 2. Illustrates 24,720 cells were captured in six HIVE™ devices. The cell types processed include granulocytes such as neutrophils, eosinophils, and basophils.

A researcher has 10 mL of fresh urine with only 10,000 cells total. With their current single-cell technology, they have to concentrate 10 mL to less than 100 µL. With the HIVE™ device, they can load their entire sample without any risk of losing cells due to concentration before capture.

Facilitating Loading of Larger Sample Volumes

Other systems for single cell analysis only allow small sample loading volumes, typically around 50 μL. To ensure you are not missing critical information available in the primary sample, the HIVE™ scRNAseq solution allows you to load much larger volumes of up to 4 mL.

Delivering Flexible & Scalable Workflows

The HIVE™ scRNAseq workflow reduces experimental and inter-site variability seen in other single cell analysis platforms. The workflow also delivers flexibility of processing location and throughput. The samples can be easily processed where they are collected or stored and shipped to a central facility for processing. By allowing safe sample storage, samples can be batched to improve lab efficiency.


HIVE™ Sample Capture                
HIVE™ scRNAseq Sample Capture Kit

  • 8 HIVE™ devices

HIVE™ Sample Processing
HIVE™ scRNAseq Processing Kit

  • Reagents to process HIVE™ devices and construct libraries for 8 samples.

HIVE™ scRNAseq Index Plate

  • Index primers to multiplex 96 libraries

HIVE™ Accessories

HIVE™ scRNAseq Starter Bundle

  • Index plate (96 rxns)
  • HIVE™ accessories (1 x closure tool, 1 x filter plate adapter)
  • Cell surrogates (4 rxns, needed for training only)
  • Molecular controls (4 rxns, needed for training/verification only)
  • Vacuum kit (1 x container vac trap, 1 x assembled gauge, 1 x manifold)
  • Plate kit (1 x 96-well filter plate, 1 x 96 deep well plate, 5 x 96 full height PCR plate, foil, and clear plate seals)
  • Lysis boxes (2 x reusable boxes)

HIVE™ Sample Analysis
BeeNet™ Software

Getting Started with HIVE™ scRNAseq Solution

Visit the Honeycomb Customer Portal to access written and video protocols and download software

HIVE scRNAseq Solution: A Case Study Demonstrating Sample Stability & Fragile Cell Recovery

Expand the Possibilities for Single Cell Transcriptional Profiling with the HIVE scRNAseq Solution

Single Cell Collection FAQs:

Q. How long can I store a cell-loaded HIVE™ device?
A. The HIVE™ device is currently verified for up to two weeks of storage at -20°C, and has been successfully tested with filtered blood for up to five months of storage at -20°C.

Q. How many samples can I process at once and how long does it take?
A. The HIVE™ workflow offers a high degree of flexibility, as each sample is independent. 1 to 24 samples can be worked with in parallel and can be processed and ready for sequencing in 1.5 days.

Q. How many cells can be loaded per HIVE™ device?
A. Loading ~15,000 cells per HIVE™ device is recommended, though the loading range is 500-30,000 cells per device.

Q. What is the sample loading volume?
A. The HIVE™ device’s loading capacity is 1 – 4 mL. Loading 1 mL is recommended. If your sample volume is below 1 mL, you can use enough fresh cell media to adjust the sample volume before loading.

Q. What sample types can I use?
A. The HIVE™ scRNAseq solution can be used with eukaryotic cells containing mRNA transcripts with 3’ poly-A tails. A variety of mammalian cell types have been tested; verified primary cells and cell lines include human filtered blood, PBMCs, and mouse splenocytes.

Sequencing & Software FAQs:

Q. What sequencing platform do you recommend?
A. The HIVE™ scRNAseq Solution is compatible with Illumina® sequencing platforms capable of custom dual index paired-end sequencing. The Illumina® NovaSeq® and NextSeq® 500/550 platforms are reccomended.

Q. Are custom sequencing and index primers provided with the kit?
A. Yes, they are included and are compatible with Illumina® NovaSeq® platform v1.5 and the Illumina® NextSeq® platform v2.0 (or later).

Q. What analysis software is provided?
A. Honeycomb’s proprietary BeeNet™ software is available to customers free of charge. Please visit the Honeycomb® Customer Portal for more information.

Expand your possibilities with enhanced single cell transcriptional profiling

For research use only. Not for use in diagnostic procedures.