ArticleProceedings of the National Academy of Sciences of the United States of America2023
mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 17 citations in OpenAlex.
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.PLoS computational biology · 2025Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.Research square · 2025Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.bioRxiv : the preprint server for biology · 2025Article
- Genetic associations of plasma metabolites with immune cells in hyperthyroidism revealed by Mendelian randomization and GWAS-sc-eQTLs xQTLbiolinks analysis.Scientific reports · 2025Article
- MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants.Genomics, proteomics & bioinformatics · 2024Article
- Single-cell mitochondrial sequencing reveals low-frequency mitochondrial mutations in naturally aging mice.Aging cell · 2024Article
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch effects. Exogenous barcodes or genome-wide RNA mutations can be used to demultiplex pooled scRNA-seq data, but they are experimentally or computationally challenging and limited in scope. Mitochondrial genomes are small but diverse, providing concise genotype information. We developed "mitoSplitter," an algorithm that demultiplexes samples using mitochondrial RNA (mtRNA) variants, and demonstrated that mtRNA variants can be used to demultiplex large-scale scRNA-seq data. Using affordable computational resources, mitoSplitter can accurately analyze 10 samples and 60,000 cells in 6 h. To avoid the batch effects from separated experiments, we applied mitoSplitter to analyze the responses of five non-small cell lung cancer cell lines to BET (Bromodomain and extraterminal) chemical degradation in a multiplexed fashion. We found the synthetic lethality of
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