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在scRNA-Seq中的牛品种对肌肉纤维类型解卷的影响:软件工具的比较

Raphael P Moreira^1,2, Marcelo R Vicari³, Henrique A Mulim²

¹Graduate Program in Genetics, Federal University of Paraná, Curitiba 81531-980, PR, Brazil.

Biotech (Basel (Switzerland))

|August 22, 2025

概括

选择合适的牛品种作为参考数据对于准确的肌肉纤维类型估计是非常重要的. 不同的品种对结果产生重大影响,影响畜牧基因组学研究.

科学领域:

基因组学
生物信息学
畜牧业科学

背景情况:

大量RNA测序提供了全转录组数据,但缺乏细胞类型分辨率.
单细胞RNA测序 (scRNA-seq) 提供了细胞细节,但成本高昂.
解卷法从大量数据中估计细胞比例,但准确性取决于参考数据和软件.

研究的目的:

调查牛品种对肌肉纤维类型比例解卷分析的参考scRNA-seq数据的影响.
将四个解卷软件工具 (CIBERSORTx,Cellanneal,DeconvR-NNLS,DeconvR-RLM) 的性能进行比较.

主要方法:

从霍尔斯坦弗里斯牛的*Longissimus dorsi*肌肉中分析大量的RNA测序数据.
使用了来自布拉曼和瓦格尤牛的scRNA-seq参考数据.
使用Kruskal-Wallis和Dunn的测试来评估统计学意义.

主要成果:

参考scRNA-seq数据的品种显著影响了IIa和IIx类型肌肉纤维的估计比例.
在四种解卷方法中观察到肌肉纤维类型比例的差异.
这项研究首次证明了品种特异性对牛的脱结果的影响.

结论:

参考scRNA-seq数据集的牛品种选择是影响解卷精度的关键因素.
未来的畜牧基因组学解卷研究必须考虑参考和目标数据集之间的品种兼容性.
仔细考虑品种匹配对于可靠的细胞类型比例估计至关重要.

关键词:

布拉汉人荷尔斯坦州长背部瓦格尤肌纤维的组成转录组

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