Integration of whole transcriptome spatial profiling with protein markers

Spatial transcriptomics and proteomics provide complementary information that independently transformed our understanding of complex biological processes. However, experimental integrations of these modalities are limited. To overcome this, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for high-throughput simultaneous integration of spatial transcriptomics and protein profiling. Compared to unimodal measurements, SPOTS substantially improves signal resolution and cell clustering and enhances the discovery power in differential gene expression analysis across tissue regions. Multimodal spatial profiling of whole transcriptomes and extracellular proteins in mouse spleen and breast cancer.空间转录组学与蛋白质组学可提供互补信息，二者均独立推动了我们对复杂生物过程的认知革新。然而，当前针对这两类分析模态的实验整合仍存在诸多局限。为攻克这一难题，我们开发了空间蛋白质与转录组测序（Spatial PrOtein and Transcriptome Sequencing, SPOTS）技术，可实现空间转录组学与蛋白质表达谱分析的高通量同步整合。相较于单模态检测手段，SPOTS可显著提升信号分辨率与细胞聚类效果，并增强跨组织区域差异基因表达分析的发现效能。本数据集涵盖小鼠脾脏与乳腺癌样本的全转录组及细胞外蛋白质的多模态空间表征分析数据。