Abstract：
Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.
摘要：
作为探索细胞多样性和组织结构的工具，mRNAs的多重空间分析最近获得了吸引力。我们建议一个敏感的，开源,简单灵活的方法生成数百个基因的原位表达图谱。我们利用挂锁探针在mRNA上的直接连接，结合滚环扩增和基于杂交的原位组合条形码，为了实现高检测效率，高吞吐量和大复用。我们在许多物种中验证了该方法，并显示其与抗体染色等正交方法结合使用，强调其对发育和组织生物学研究的潜在价值。最后,我们提供了一个端到端的计算工作流程，涵盖了探针设计的步骤，图像处理,数据提取,细胞分割，细胞类型的聚类和注释。通过更轻松地访问高通量空间分辨转录组学，我们希望鼓励多样化的应用和探索广泛的生物学问题。
