ADT规范:在CITE-seq数据集中强有力的整合单细胞蛋白质测量
Ye Zheng1,2, Daniel P Caron3, Ju Yeong Kim2
1Department of Bioinformatics and Computational Biology, Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Nature communications
|July 2, 2025
概括
ADTnorm是一种新的方法,它将通过测序 (CITE-seq) 来实现转录组和表皮细胞的细胞索引数据的规范化和整合. 它有效地消除了批量效应,并改善了用于大规模生物分析的细胞类型识别.
科学领域:
- 单细胞多组组分分析.
- 免疫基因组学和计算生物学
背景情况:
- 通过测序 (CITE-seq) 进行转录组和表皮细胞的细胞索引,将单细胞RNA测序与表面蛋白质检测结合起来.
- 在CITE-seq中,抗体衍生标签 (ADT) 提供了可靠的蛋白质定量,但容易受到抗体染色变化的批量影响.
- 这些批量效应掩盖了生物信号,阻碍了细胞类型的识别,并阻碍了跨数据集的比较.
研究的目的:
- 引入ADTnorm,这是一种专门为CITE-seq实验中的ADT丰度数据设计的新型规范化和整合方法.
- 证明ADTnorm在消除技术差异和提高CITE-seq数据在不同数据集中的可解释性方面的有效性.
- 为自动化值测定和抗体质量评估提供工具,促进CITE-seq数据分析和优化.
主要方法:
- 开发和应用ADTnorm,一种用于规范化和整合ADT表达式数据的计算方法.
- 使用13个公共CITE-seq数据集对14种现有方法进行ADTnorm的比较.
- 在抗体定位研究,COVID-19 CITE-seq 数据和造血原体数据集上验证ADTnorm.
主要成果:
- ADTnorm 准确地对齐了不同批次的细胞种群,有效地消除了技术变异.
- 与现有的规范化技术相比,该方法显著改善了细胞类型的分离和可解释性.
- ADTnorm促进了多样化的CITE-seq数据集的整合,使得在地图层面进行分析和发现新型表型相关标记.
结论:
- ADTnorm提供了一个强大的解决方案,用于规范化和集成CITE-seq ADT数据,克服批量效应的挑战.
- 该方法增强了CITE-seq在细胞类型识别,交叉研究比较和大规模生物发现方面的实用性.
- ADTnorm的集成工具支持抗体验证和数据分析,扩大其在生物研究中的应用.
相关概念视频
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