biostudies-literatureUnknown53(2)De Simone MGenentechThis study examined nine prominent commercially available single-cell RNA sequencing (scRNA-seq) kits across four technology groups. Each kit was characterized using peripheral blood mononuclear cells (PBMCs) from a single donor, which enabled consistent assessment of factors such as analytical performance, protocol duration and cost. The Chromium Fixed RNA Profiling kit from 10× Genomics, with its probe-based RNA detection method, demonstrated the best overall performance. The Rhapsody WTA kit from Becton Dickinson exhibited a balance between performance and cost. Importantly, we introduce the read utilization metric, which differentiates scRNA-seq kits based on the efficiency of converting sequencing reads into usable counts. Thus, read utilization is an important feature that substantiaNucleic acids researchgkae1186https://www.ebi.ac.uk/biostudies/studies/S-EPMC11754665biostudies-literatureA comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies.PMC11754665Darmanis SAu-Yeung AShi MHoover JMenon HVaidya SLiang YWu BXavier-Magalhaes ABennett HMChen CLear SLau JKurdoglu AO'Gorman WELund JMLe DDe Simone MModrusan ZfalseA comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies.This study examined nine prominent commercially available single-cell RNA sequencing (scRNA-seq) kits across four technology groups. Each kit was characterized using peripheral blood mononuclear cells (PBMCs) from a single donor, which enabled consistent assessment of factors such as analytical performance, protocol duration and cost. The Chromium Fixed RNA Profiling kit from 10× Genomics, with its probe-based RNA detection method, demonstrated the best overall performance. The Rhapsody WTA kit from Becton Dickinson exhibited a balance between performance and cost. Importantly, we introduce the read utilization metric, which differentiates scRNA-seq kits based on the efficiency of converting sequencing reads into usable counts. Thus, read utilization is an important feature that substantia2025-01-01T00:00:00Z2025 Jan2025-04-05T10:18:47.04Z2025-04-05T10:18:47.04ZS-EPMC117546653967538010.1093/nar/gkae1186