ArticleAmerican journal of respiratory cell and molecular biology2020
Single-Nucleus RNA-Sequencing Profiling of Mouse Lung. Reduced Dissociation Bias and Improved Rare Cell-Type Detection Compared with Single-Cell RNA Sequencing.
Article in American journal of respiratory cell and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 82 citations in OpenAlex.
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- Apelin analog treatment reverses severe pulmonary arterial hypertension and right ventricular heart failure.JCI insight · 2026Article
- Co-optation of the regenerative role of type 2 alveolar cells in distal lung repair in mice by terminal airway epithelial cells in humans.bioRxiv : the preprint server for biology · 2026Article
- Single-nucleus RNA sequencing identifies conserved structural cell programs in allergic lung inflammation.The journal of allergy and clinical immunology. Global · 2026Article
- Latent transforming growth factor binding protein-2 (LTBP2), an IPF biomarker of clinical decline, promotes TGF-beta signaling and lung fibrosis in mice.American journal of respiratory cell and molecular biology · 2026Article
- Spatially Resolved Heterogeneity of Lymphatic Vasculature in the Adult Lung-Brief Report.Arteriosclerosis, thrombosis, and vascular biology · 2026Article
- From identity to function: unveiling the cellular complexity of hypothalamic feeding circuits.Reviews in endocrine & metabolic disorders · 2026Review
- Reduction in Hepatic Phosphatidylcholine Biosynthesis Promotes MASH Through Copper Deficiency.bioRxiv : the preprint server for biology · 2026Article
- IL-11 acts as an alarmin-like pro-inflammatory mediator regulating mucosal responses during helminth infection.Mucosal immunology · 2026Article
- Aberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary disease.Nature genetics · 2026Article
- Elucidating a Myofibroblast-dominated Fibrotic Niche in Crohn's Disease-associated Fibrostenosis Through High-resolution Spatial Transcriptomics.Cellular and molecular gastroenterology and hepatology · 2026Article
- Cellular heterogeneity and multicellular mechanisms in the pathogenesis of late-life depression: insights from single-cell and spatial multi-omics.Frontiers in immunology · 2026Review
- Distinct populations of lung capillary endothelial cells and their functional significance.Communications biology · 2025Article
- Writing the Engram: Epigenetic Mechanisms of Memory Allocation.Journal of neurochemistry · 2025Review
- snRNA-seq reveals key transcription factors in the inflammatory response of microglia after intracerebral hemorrhage.Scientific reports · 2025Article
- Comparative Single-Cell Transcriptomics Uncovers Shared and Distinct Molecular Signatures in Cystic Fibrosis and Primary Ciliary Dyskinesia.bioRxiv : the preprint server for biology · 2025Article
- Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow.bioRxiv : the preprint server for biology · 2025Article
- Latent transforming growth factor binding protein-2 (LTBP2), an IPF biomarker of clinical decline, promotes TGF-beta signaling and lung fibrosis in mice.bioRxiv : the preprint server for biology · 2025Article
- Rapid Dissection and Dissociation of the Mouse Olfactory Epithelium for Single-Nucleus Suspensions.Journal of visualized experiments : JoVE · 2025Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell RNA sequencing (scRNASeq) has advanced our understanding of lung biology, but its utility is limited by the need for fresh samples, loss of cell types by death or inadequate dissociation, and transcriptional stress responses induced during tissue digestion. Single-nucleus RNA sequencing (snRNASeq) has addressed these deficiencies in other tissues, but no protocol exists for lung tissue. We present a snRNASeq protocol and compare its results with those of scRNASeq. Two nuclear suspensions were prepared in lysis buffer on ice while one cell suspension was generated using enzymatic and mechanical dissociation. Cells and nuclei were processed using the 10× Genomics platform, and sequencing data were analyzed by Seurat. A total of 16,110 single-nucleus and 11,934 single-cell transcriptomes were generated. Gene detection rates were equivalent in snRNASeq and scRNASeq (∼1,700 genes and 3,000 unique molecular identifiers per cell) when mapping intronic and exonic reads. In the combined data, 89% of epithelial cells were identified by snRNASeq versus 22.2% of immune cells. snRNASeq transcriptomes are enriched for transcription factors and signaling proteins, with reduction in mitochondrial and stress-response genes. Both techniques improved mesenchymal cell detection over previous studies. Homeostatic signaling relationships among alveolar cell types were defined by receptor-ligand mapping using snRNASeq data, revealing interplay among epithelial, mesenchymal, and capillary endothelial cells. snRNASeq can be applied to archival murine lung samples, improves dissociation bias, eliminates artifactual gene expression, and provides similar gene detection compared with scRNASeq.
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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.