ArticleNucleic acids research2025
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- SignifiKANTE: efficient P-value computation for gene regulatory networks.Bioinformatics (Oxford, England) · 2026Article
- Article
- Increasing usable reads in RNA-seq protocols.iScience · 2026Article
- Genomics in containment: BSL-4-compatible workflows enable high-resolution genomic and transcriptomic analyses of Risk Group 4 viruses.iScience · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- scKanFormer: A Transformer-KAN framework with biologically informed attention for cell type annotation in large-scale scRNA-seq data.PLoS computational biology · 2026Article
- A novel biclustering algorithm for mining m6A co-methylation patterns based on beta-binomial distribution and data screening strategy.PLoS computational biology · 2026Article
- Harvesting more reads from single-cell combinatorial barcoding data with scarecrow.Bioinformatics (Oxford, England) · 2026Article
- Dissecting Normal and Abnormal Human Kidney Development Using Multiomics.Journal of the American Society of Nephrology : JASN · 2026Review
- Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.NAR genomics and bioinformatics · 2026Article
- Decoding the archipelago: single-cell biomarkers rechart the molecular geography of acute myeloid leukemia.Cell communication and signaling : CCS · 2026Review
- Genome-wide single-cell perturbation screens with VIPerturb-seq.bioRxiv : the preprint server for biology · 2026Article
- CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs.Frontiers in bioinformatics · 2026Article
- Single-cell analysis of matched FFPE and frozen tissue samples reveals comparable resolution of intratumoural heterogeneity.Frontiers in genetics · 2026Article
- Spatially resolved gene expression analysis illuminates location-specific functions in the reef-building coral Pocillopora acuta.PloS one · 2026Article
- Massively Scalable Single-cell Multiomic Profiling of T Cell Repertoire with REFLEX.Research square · 2025Article
- REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell Resolution to Catapult Exploration of T-cell Derived Immunity.bioRxiv : the preprint server for biology · 2025Article
- Leveraging two novel droplet-based single-cell RNA Sequencing platforms: a comparative study with 10x genomics.BMC genomics · 2025Article
- Comparison of single-cell RNA-seq methods to enable transcriptome profiling of neutrophils in clinical samples.Cell reports methods · 2025Article
- Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
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 substantially impacts sensitivity and cost. With data from 169, 262 cells, our work provides a comprehensive comparison of commercial scRNA-seq technologies to facilitate the effective implementation of single-cell studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.