ArticleCellular and molecular life sciences : CMLS2021
Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias.
Article in Cellular and molecular life sciences : CMLS, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Organ-Specific and Conserved Regulatory Logic Orchestrates Gene Expression in the Embryonic Mesothelium.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Structural and transcriptomic alterations underlying the progression of aortic dissection in Fbn1Scientific reports · 2026Article
- Single-cell transcriptomics reveals lipid metabolism reprogramming in macrophages in vitro during early stages of Leishmania donovani infection.Parasites & vectors · 2026Article
- Surface Marker Identification to Capture Live Circulating Tumor Cells in Metastatic Triple-Negative Breast Cancer.Cancer research communications · 2026Article
- Single cell and spatial transcriptomic profiling of the type 2 diabetic coronary microcirculation and myocardium.Basic research in cardiology · 2025Article
- Cyclin A2 induces cytokinesis in human adult cardiomyocytes and drives reprogramming in mice.NPJ Regenerative medicine · 2025Article
- Circular RNAs in Cardiovascular Physiopathology: From Molecular Mechanisms to Therapeutic Opportunities.International journal of molecular sciences · 2025Review
- Article
- Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications.Genomics & informatics · 2025Review
- Cardiac conduction system regeneration prevents arrhythmias after myocardial infarction.Nature cardiovascular research · 2025Article
- Dissecting the Heterogeneity of Senescent Cells Through CITE-seq Integration.Methods in molecular biology (Clifton, N.J.) · 2025Article
- DDR1 as a key prognostic biomarker in non-small cell lung cancer: identification, validation, and potential therapeutic implications.Frontiers in immunology · 2025Article
- Advancements in Omics and Breakthrough Gene Therapies: A Glimpse into the Future of Peripheral Artery Disease.Annals of vascular surgery · 2024Review
- A new paradigm for generating high-quality cardiac pacemaker cells from mouse pluripotent stem cells.Signal transduction and targeted therapy · 2024Article
- Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva.International journal of legal medicine · 2024Article
- DbhNature communications · 2023Article
- Single-cell RNA sequencing of murine hearts for studying the development of the cardiac conduction system.Scientific data · 2023Article
- New Approaches in Heart Research: Prevention Instead of Cardiomyoplasty?International journal of molecular sciences · 2023Review
- scRNA-seq data analysis method to improve analysis performance.IET nanobiotechnology · 2023Review
- Temporal tracking of microglial and monocyte single-cell transcriptomics in lethal flavivirus infection.Acta neuropathologica communications · 2023Article
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7 authors.
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Abstract
Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to "low quality" potentially leading to data misinterpretation. Common standard quality control parameters involve the number of detected genes, transcripts per cell, and the fraction of transcripts from mitochondrial genes. While cutoffs for transcripts and genes per cell are usually user-defined for each experiment or individually calculated, a fixed threshold of 5% mitochondrial transcripts is standard and often set as default in scRNA-seq software. However, this parameter is highly dependent on the tissue type. In the heart, mitochondrial transcripts comprise almost 30% of total mRNA due to high energy demands. Here, we demonstrate that a 5%-threshold not only causes an unacceptable exclusion of cardiomyocytes but also introduces a bias that particularly discriminates pacemaker cells. This effect is apparent for our in vitro generated induced-sinoatrial-bodies (iSABs; highly enriched physiologically functional pacemaker cells), and also evident in a public data set of cells isolated from embryonal murine sinoatrial node tissue (Goodyer William et al. in Circ Res 125:379-397, 2019). Taken together, we recommend omitting this filtering parameter for scRNA-seq in cardiovascular applications whenever possible.
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