ReviewCellular and molecular life sciences : CMLS2022
Sample-multiplexing approaches for single-cell sequencing.
Review in Cellular and molecular life sciences : CMLS, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- CMDdemux: an efficient single cell demultiplexing method.Nucleic acids research · 2026Article
- fastdemux: Robust SNP-based demultiplexing of single-cell population genomics data.bioRxiv : the preprint server for biology · 2026Article
- Semantic alignment of the German Human Genome-Phenome Archive metadata model in Europe's genomics field.Scientific data · 2026Article
- Dynamic heterogeneity towards drug resistance in AML cells is primarily driven by epigenomic mechanism unveiled by multi-omics analysis.Journal of advanced research · 2026Article
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- OddSNP: a predictive framework for optimizing multiplexed single-cell RNA-seq experiments.bioRxiv : the preprint server for biology · 2025Article
- Next generation sequencing and beyond: a review of genomic sequencing methods.Functional & integrative genomics · 2025Article
- Recovery of biological signals lost in single-cell batch integration with CellANOVA.Nature biotechnology · 2025Article
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.bioRxiv : the preprint server for biology · 2025Article
- Acquired resistance in cancer: towards targeted therapeutic strategies.Nature reviews. Cancer · 2025Review
- Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer.International journal of molecular sciences · 2025Review
- Bridging epigenomics and tumor immunometabolism: molecular mechanisms and therapeutic implications.Molecular cancer · 2025Review
- Toti-N-glycan Recognition Enables Universal Multiplexed Single-Nucleus RNA Sequencing.Research (Washington, D.C.) · 2025Article
- MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants.Genomics, proteomics & bioinformatics · 2024Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- A hybrid demultiplexing strategy that improves performance and robustness of cell hashing.Briefings in bioinformatics · 2024Article
- q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics.Communications biology · 2024Article
- demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs.GigaScience · 2024Article
- Microfluidic design in single-cell sequencing and application to cancer precision medicine.Cell reports methods · 2023Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Single-cell sequencing is widely used in biological and medical studies. However, its application with multiple samples is hindered by inefficient sample processing, high experimental costs, ambiguous identification of true single cells, and technical batch effects. Here, we introduce sample-multiplexing approaches for single-cell sequencing in transcriptomics, epigenomics, genomics, and multiomics. In single-cell transcriptomics, sample multiplexing uses variants of native or artificial features as sample markers, enabling sample pooling and decoding. Such features include: (1) natural genetic variation, (2) nucleotide-barcode anchoring on cellular or nuclear membranes, (3) nucleotide-barcode internalization to the cytoplasm or nucleus, (4) vector-based barcode expression in cells, and (5) nucleotide-barcode incorporation during library construction. Other single-cell omics methods are based on similar concepts, particularly single-cell combinatorial indexing. These methods overcome current challenges, while enabling super-loading of single cells. Finally, selection guidelines are presented that can accelerate technological application.
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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.