SCSMRD: A database for single-cell skeletal muscle regeneration
FENG Xi-kang1,XIE Chun-di2, LI Yong-yao3, WANG Zi-shuai3#, BAI Li-jing3#
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
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.
Received: 07 December 2021
Accepted: 27 February 2022
Fund:
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).
About author: #Correspondence WANG Zi-shuai, E-mail: wangzishuai@caas.cn; BAI Li-jing, E-mail: bailijing@caas.cn
FENG Xi-kang, XIE Chun-di, LI Yong-yao, WANG Zi-shuai, BAI Li-jing.
2023.
SCSMRD: A database for single-cell skeletal muscle regeneration. Journal of Integrative Agriculture, 22(3): 864-871.
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