Journal article
Systematic comparison of sequencing-based spatial transcriptomic methods
Y You, Y Fu, L Li, Z Zhang, S Jia, S Lu, W Ren, Y Liu, Y Xu, X Liu, F Jiang, G Peng, A Sampath Kumar, ME Ritchie, X Liu, L Tian
Nature Methods | Published : 2024
Open access
Abstract
Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare 11 sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, signif..
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Awarded by National Natural Science Foundation of China
Funding Acknowledgements
We thank Y. Cao for providing supports in data preprocessing. We thank members of the Tian and Liu laboratories for helpful discussions. We thank Y. Li for his support to the Tian Laboratory and to this project. We thank G. Cao for the helpful discussion. This work was supported by the National Natural Science Foundation of China (grant nos. 32370784 and 22DAA01467), the National Key R&D Program of China (grant no. 2022YFA1105700), Guangzhou National Laboratory (grant no. YW-YFYJ0301) and the Westlake Education Foundation.