ArticleNeuron2022
Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets.
Article in Neuron, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Somatic mutations and single-nucleus transcriptomics reveal uniquely human properties of neuronal aging.bioRxiv : the preprint server for biology · 2026Article
- Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping.bioRxiv : the preprint server for biology · 2026Article
- Systematic benchmarking of ambient RNA decontamination tools to advance precision in single-cell transcriptomic analysis.Nature communications · 2026Article
- A who's who of cell types in skeletal muscle.Communications biology · 2026Review
- Distinct single-nucleus RNA-seq changes among non-neuronal cells in ADNC, LATE-NC, and mixed pathologies.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- SETDB1 modulates neuroinflammation in the mouse cortex by regulating neuronal P2rx7 expression.Molecular psychiatry · 2026Article
- Single-nucleus transcriptomics-based drug screening platform for focal cortical dysplasia.Molecular psychiatry · 2026Article
- CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.Cell genomics · 2026Article
- Protocol to maximize single-nuclei multiome library complexity for limited primary tissues via optimized sample preparation and library synthesis.STAR protocols · 2026Article
- Charting the human-specific properties of gene expression networks in the infant prefrontal cortex.Science advances · 2026Article
- Comparative analysis of the cellular landscape in mammalian striatum.Nature communications · 2026Article
- High-quality acinar cell isolation enables single-cell analysis of healthy and injured pancreas.Cell reports methods · 2026Article
- Spatiotemporal dynamics of adoptively transferred stem-like CD8bioRxiv : the preprint server for biology · 2026Article
- Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.Cell reports methods · 2026Article
- Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex.bioRxiv : the preprint server for biology · 2026Article
- Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis.Circulation research · 2026Article
- Microglial state transitions are constrained by developmental and metabolic checkpoints.Frontiers in cellular neuroscience · 2026Review
- Context-tuned strategies for marker selection precision in neuronal studies.Frontiers in neuroscience · 2026Review
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- DAP12 deletion reduces neuronal SLIT2 and demyelination and enhances brain resilience in female tauopathy mice.Molecular neurodegeneration · 2025Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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Abstract
Ambient RNA contamination in single-cell and single-nuclei RNA sequencing (snRNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain snRNA-seq datasets have a nuclear or non-nuclear origin with distinct gene set signatures. Both ambient RNA signatures are predominantly neuronal, and we find that some previously annotated neuronal cell types are distinguished by ambient RNA contamination. We detect pervasive neuronal ambient RNA contamination in all glial cell types unless glia and neurons are physically separated prior to sequencing. We demonstrate that this contamination can be removed in silico and show that previous single-nuclei RNA-seq-based annotations of immature oligodendrocytes are glial nuclei contaminated with ambient RNAs. After ambient RNA removal, we detect rare, committed oligodendrocyte progenitor cells not annotated in most previous adult human brain datasets. Together, these results provide an in-depth analysis of ambient RNA contamination in brain single-nuclei datasets.
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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.