JIA-2021-2507  SCSMRD：小鼠单细胞骨骼肌再生数据库

doi:10.1016/j.jia.2022.08.108

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (3): 864-871.DOI: 10.1016/j.jia.2022.08.108

JIA-2021-2507 SCSMRD：小鼠单细胞骨骼肌再生数据库

收稿日期:2021-12-07 接受日期:2022-02-27 出版日期:2023-03-20 发布日期:2022-02-27

SCSMRD: A database for single-cell skeletal muscle regeneration

FENG Xi-kang¹,XIE Chun-di², LI Yong-yao³, WANG Zi-shuai^3#, BAI Li-jing^3#

¹ School of Software, Northwestern Polytechnical University, Xi’an 710072, P.R.China
² Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
³ Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, P.R.China

Received:2021-12-07 Accepted:2022-02-27 Online:2023-03-20 Published:2022-02-27
About author:#Correspondence WANG Zi-shuai, E-mail: wangzishuai@caas.cn; BAI Li-jing, E-mail: bailijing@caas.cn
Supported by:
This research was supported by the National Natural Science Foundation of China (31972539 and 32102513), the Science, Technology, and Innovation Commission of Shenzhen Municipality, China (JCYJ20180306173644635), the Fundamental Research Funds for the Central Universities, China (G2020KY05109), the Natural Science Basic Research Program of Shaanxi Province, China (2022JQ-644), and the Basic Research Programs of Taicang, China (TC2021JC14).

摘要/Abstract

摘要：

产肉量是家畜（包括猪、牛和羊等）重要生产力指标和经济性状之一。产肉量是典型的数量性状，受多基因调控。影响产肉性状形成的基础是骨骼肌组织的生长和发育。骨骼肌生长发育是一个复杂的生物学过程，包括成肌细胞的形成、增殖、凋亡、迁移、融合和分化。骨骼肌损伤修复过程中基因表达变化与初始胚胎发育过程类似，完美的重现了上述骨骼肌生长发育过程。因此，骨骼肌损伤修复被认为是研究骨骼肌生长发育的理想模型。鉴定骨骼肌损伤修复过程中调节肌生成相关重要基因和特定调控网络，能够为家畜产肉量等重要经济生产性状形成的分子机制提供理论支持。已有研究表明，骨骼肌功能障碍与肌营养不良、萎缩，2型糖尿病和衰老相关的肌肉减少症等500多种人类疾病密切相关。因此，深入了解骨骼肌损伤修复过程中基因表达差异以及调控网络，也能为再生医学提供新的药物靶点，这些靶点可以增强或诱导功能性骨骼肌从头生成，以治疗先天性缺失或创伤性组织损失。

近些年针对小鼠骨骼肌损伤修复的单细胞RNA 测序(scRNA-seq)陆续产出了大量数据，但是，从单细胞水平研究骨骼肌再生过程中基因表达变化的数据库尚未构建。本研究汇集了七个关键再生时间点和正常骨骼肌单细胞RNA-seq数据（共计超过 105,000 个细胞）开展一系列生物信息分析，包括细胞聚类、细胞类型注释、细胞周期识别、骨骼肌卫星细胞发育状态转换轨迹和调节单元动态表达图谱构建等。开发构建了SCSMRD （https://scsmrd.fengs-lab.com）数据库，界面友好，操作简单，提供了多种搜索功能，包括，用户感兴趣基因在不同细胞类型和损伤修复不同时间点的动态表达图谱，不同细胞类型中特异调节单元网络动态变化和用户感兴趣基因基因在骨骼肌卫星细胞发育状态转变过程中的表达模式等。SCSMRD数据库为研究人员在单细胞层面研究骨骼肌损伤修复的转录组动态变化提供了可靠的生信技术支撑和数据支持。

Abstract:

Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved. Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles. Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration. However, a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking. Here, we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database, the Single-cell Skeletal Muscle Regeneration Database (SCSMRD). SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process. It also provides a network to show the activity of regulons in different cell types at different time points. Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration. This database is freely available at https://scsmrd.fengs-lab.com.

Key words: scRNA-Seq , skeletal muscle regeneration , database , regulon network , pseudotime

. JIA-2021-2507 SCSMRD：小鼠单细胞骨骼肌再生数据库[J]. Journal of Integrative Agriculture, 2023, 22(3): 864-871.

FENG Xi-kang, XIE Chun-di, LI Yong-yao, WANG Zi-shuai, BAI Li-jing. SCSMRD: A database for single-cell skeletal muscle regeneration[J]. Journal of Integrative Agriculture, 2023, 22(3): 864-871.

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JIA-2021-2507 SCSMRD：小鼠单细胞骨骼肌再生数据库

SCSMRD: A database for single-cell skeletal muscle regeneration

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