<br>指导构建人和小鼠肺的单细胞参考,Nature Communications

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指导构建人和小鼠肺的单细胞参考
Nature Communications ( IF 14.7 ) Pub Date : 2023-07-29 , DOI: 10.1038/s41467-023-40173-5
Minzhe Guo _{1,

2} , Michael P Morley _{3,

4,

5} , Cheng Jiang ₁ , Yixin Wu ₁ , Guangyuan Li ₆ , Yina Du ₁ , Shuyang Zhao ₁ , Andrew Wagner ₁ , Adnan Cihan Cakar ₁ , Michal Kouril ₆ , Kang Jin ₆ , Nathan Gaddis ₇ , Joseph A Kitzmiller ₁ , Kathleen Stewart _{3,

4} , Maria C Basil _{3,

4} , Susan M Lin _{3,

4} , Yun Ying _{3,

4} , Apoorva Babu _{3,

4} , Kathryn A Wikenheiser-Brokamp _{1,

8,

9} , Kyu Shik Mun _{10,

11} , Anjaparavanda P Naren ₁₀ , Geremy Clair ₁₂ , Joshua N Adkins ₁₂ , Gloria S Pryhuber ₁₃ , Ravi S Misra ₁₃ , Bruce J Aronow _{2,

6} , Timothy L Tickle ₁₄ , Nathan Salomonis _{2,

6} , Xin Sun _{15,

16} , Edward E Morrisey _{3,

4,

5} , Jeffrey A Whitsett _{1,

2} , , Yan Xu _{1,

2,

6}

Affiliation

The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.
Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
RTI International, Durham, NC, 27709, USA.
Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA.
Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
Department of Pediatrics Division of Neonatology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
Data Sciences Platform, The Broad Institute, Cambridge, MA, 02142, USA.
Department of Pediatrics, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
Department of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.

准确的细胞类型识别是单细胞数据分析中的关键和限速步骤。研究界非常需要具有全面细胞类型、可重复且功能验证的细胞身份以及通用命名法的单细胞参考，以实现自动细胞类型注释、数据集成和数据共享。在这里，我们开发了一个计算管道，利用 LungMAP CellCards 作为字典来整合 104 个人类肺部和 17 个小鼠肺部样本的单细胞转录组数据集，以构建正常人类和小鼠肺部的 LungMAP 单细胞参考 (CellRef)。 CellRefs 定义了 48 种人类和 40 种小鼠肺细胞类型，这些细胞类型根据不同的解剖位置和发育时间点进行分类。我们使用多种独立方法和测试数据证明了 LungMAP CellRefs 的准确性和稳定性，及其对正常和患病肺部的自动细胞类型注释的实用性。我们开发用户友好的 Web 界面，以便轻松访问和最大限度地利用 LungMAP CellRefs。

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更新日期：2023-07-29

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