Si-scRNA-seq: unlocking stable single-cell transcriptomics under am-bient conditions

Abstract

Single-cell RNA sequencing faces critical challenges due to RNA instability during storage. We developed spatial-ly confined biosilicification (SCB) and Si-scRNA-seq for ambient-temperature preservation of single-cell tran-scriptomes. SCB precisely controls silica deposition using a silicification inhibitor, preventing excessive crosslink-ing and cellular aggregation. The extracellular silica network provides physical barriers while intracellular RNA-protein-silica complexes confer structural stabilization, enhancing resistance to oxidative and UV damage. Si-scRNA-seq successfully resolved cellular heterogeneity in lung, liver, and ovarian cancers after extended storage. Compatible with mainstream plat-forms at only 0.1 RMB per sample, this method eliminates cold-chain dependence, providing a practical solution for research and clinical applications.