Abstract

Objective: Single cell RNA sequencing (scRNAseq) is sensitive to degradation during sample storage and shipping. Cryopreservation causes poor cell viability, leading to poor data quality. Limiting the ability to conduct large scale studies with multiple timepoints and conditions. HIVE™ integrates stable single-cell storage and transcriptional profiling into a complete workflow enabling researchers to overcome these limitations. Methods: A fresh renal cell carcinoma biopsy was dissociated for flow cytometry, cell capture with the HIVE, and cryopreservation of the remaining sample. Cell-loaded HIVEs and cryovials were shipped to Honeycomb for processing and generation of HIVE libraries, after 2 or 20 weeks of storage. Libraries were sequenced on Illumina® platforms, and count matrix files were generated using BeeNet, Honeycomb’s software specifically designed for HIVE libraries. Seurat was used for downstream analysis of high-quality cells. Results: Cell-type proportions were matched between flow cytometry and HIVE results, indicating no bias in cell-type recovery. The sample stored in the HIVE was stable through 20 weeks and yielded 2–3× more cells with higher genes and transcripts per cell compared to the cryopreserved cells, which were immediately damaged after only 2 weeks of storage. The cryopreserved sample progressively degraded through 20 weeks of storage, destroying immune cells, including T cells, monocytes, and macrophages, biasing sample composition.Conclusions: The quantity, quality, and biological complexity of cells stored and shipped in the HIVE device are comparable to freshly processed cells. The HIVE enables single-cell studies for high-throughput screening. Detecting cell-type specificity and abundance for payloads of interest. Giving researchers the ability to process samples collected acro