MHA，一个用于男性生殖泌尿系统发育和疾病的 scRNA-seq 数据的交互式网站。

MHA, an interactive website for scRNA-seq data of male genitourinary development and disease.

机构信息

Department of Urology, Department of Interventional Medicine, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China.

Department of Andrology, Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

出版信息

Andrology. 2023 Sep;11(6):1157-1162. doi: 10.1111/andr.13402. Epub 2023 Feb 6.

DOI:10.1111/andr.13402

PMID:36710661

Abstract

BACKGROUND

The development of single-cell sequencing technology has expanded the understanding of cell heterogeneity and disease progression in the male genitourinary system. However, complex processing and unprofessional analytical annotations limit the daily use and widely sharing of published datasets.

OBJECTIVES

Single-cell sequencing data of male-specific tissues and organs.

MATERIALS AND METHODS

The data were downloaded from published studies and were processed based on the Seurat R package, including quality control, cell clustering, reduction and graph generation, and cell type annotation were differentiated by referring to the related paper or recognized cell markers. Input and visual results output through the Shiny package, which was loaded into the remote server.

RESULTS

The current version of the Male Health Atlas database includes two species (human and mouse), five male-specific tissues and organs (testis, epididymis, vas deferens, corpus cavernosum, and prostate), and eight major cell types, with a total of 57 samples and 258,428 single-cell profiles. The results were divided into two main parts: Cell Clustering and Gene Display. In Cell Clustering section, visitors are free to change cell dimensionality reduction (t-distributed stochastic neighbor embedding, or uniform manifold approximation and projection), color palette, and annotation (cell type or sample type). The Gene Display section includes a reduced dimension scatter plot, violin plot, and bubble plot. Visitors can easily view the expression characteristics of single or multiple genes, and compare the expression differences between different cell types or groups.

DISCUSSION AND CONCLUSION

Male Health Atlas is the first single-cell database website in the field of andrology and male reproduction, providing researchers with single-cell sequencing resources and an accessible tool. Male Health Atlas is freely available at http://malehealthatlas.cn/.

摘要

背景

单细胞测序技术的发展拓展了人们对男性生殖系统细胞异质性和疾病进展的认识。然而，复杂的处理过程和非专业的分析注释限制了已发表数据集的日常使用和广泛共享。

目的

男性特异性组织和器官的单细胞测序数据。

材料和方法

从已发表的研究中下载数据，并基于 Seurat R 包进行处理，包括质量控制、细胞聚类、降维和图形生成，通过参考相关论文或公认的细胞标记物对细胞类型进行注释。通过 Shiny 包输入和可视化结果输出，并加载到远程服务器中。

结果

目前的 Male Health Atlas 数据库包括两个物种（人类和小鼠）、五个男性特异性组织和器官（睾丸、附睾、输精管、阴茎海绵体和前列腺）以及八个主要细胞类型，共 57 个样本和 258428 个单细胞图谱。结果分为两个主要部分：细胞聚类和基因展示。在细胞聚类部分，访问者可以自由更改细胞维度降低（t 分布随机邻域嵌入或一致流形逼近和投影）、调色板和注释（细胞类型或样本类型）。基因展示部分包括降维散点图、小提琴图和气泡图。访问者可以轻松查看单个或多个基因的表达特征，并比较不同细胞类型或组之间的表达差异。