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Yang L, Ng YE, Sun H, Li Y, Chini LCS, LeBrasseur NK, Chen J, Zhang X. Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis. BMC Biol 2023; 21:223. [PMID: 37858214 PMCID: PMC10588107 DOI: 10.1186/s12915-023-01728-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed. RESULTS We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance. CONCLUSIONS scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.
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Affiliation(s)
- Lu Yang
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yan Er Ng
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Haipeng Sun
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ying Li
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Lucas C S Chini
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nathan K LeBrasseur
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jun Chen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Xu Zhang
- Robert and Arlene Kogod Center On Aging, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
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Kim HJ, Kim M, Kang B, Yun S, Ryeo SE, Hwang D, Kim JH. Systematic analysis of expression signatures of neuronal subpopulations in the VTA. Mol Brain 2019; 12:110. [PMID: 31829254 DOI: 10.1186/s13041-019-0530-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/26/2019] [Indexed: 12/21/2022] Open
Abstract
Gene expression profiling across various brain areas at the single-cell resolution enables the identification of molecular markers of neuronal subpopulations and comprehensive characterization of their functional roles. Despite the scientific importance and experimental versatility, systematic methods to analyze such data have not been established yet. To this end, we developed a statistical approach based on in situ hybridization data in the Allen Brain Atlas and thereby identified specific genes for each type of neuron in the ventral tegmental area (VTA). This approach also allowed us to demarcate subregions within the VTA comprising specific neuronal subpopulations. We further identified WW domain-containing oxidoreductase as a molecular marker of a population of VTA neurons that co-express tyrosine hydroxylase and vesicular glutamate transporter 2, and confirmed their region-specific distribution by immunohistochemistry. The results demonstrate the utility of our analytical approach for uncovering expression signatures representing specific cell types and neuronal subpopulations enriched in a given brain area.
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Franke WW, Domke LM, Dörflinger Y, Zimbelmann R. The cell-cell junctions of mammalian testes. III. Absence of an endothelial cell layer covering the peritubular wall of the seminiferous tubules-an immunocytochemical correction of a 50-year-old error in the literature. Cell Tissue Res 2020; 379:75-92. [PMID: 31713729 DOI: 10.1007/s00441-019-03116-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/22/2019] [Indexed: 12/28/2022]
Abstract
In the molecular biological and ultrastructural studies of the peritubular wall cells encasing the seminiferous tubules of mammalian testes, we found it necessary to characterize the outermost cell layer bordering on the interstitial space in detail. For half a century, the extremely thin cells of this monolayer have in the literature been regarded as part of a lymphatic endothelium, in particular in rodents. However, our double-label immunofluorescence microscopical results have shown that in all six mammalian species examined, including three rodent ones (rat, mouse, guinea pig), this classification is not correct: the very attenuated cells of this monolayer are not of lymphatic endothelial nature as they do not contain established endothelial marker molecules. In particular, they do not contain claudin-5-positive tight junctions, VE-cadherin-positive adherens junctions, "lymph vessel endothelium hyaluronan receptor 1" (LYVE-1), podoplanin, protein myozap and "von Willebrand Factor" (vWF). By contrast and as controls, all these established marker molecules for the lymphatic endothelial cell type are found in the endothelia of the lymph and-partly also-blood vessels located nearby in the interstitial space. Thus, our results provide evidence that the monolayer cells covering the peritubular wall do not contain endothelial marker molecules and hence are not endothelial cells. We discuss possible methodological reasons for the maintenance of this incorrect cell type classification in the literature and emphasize the value of molecular analyses using multiple cell type-specific markers, also with respect to physiology and medical sciences.
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