Rapid and signal crowdedness-robust in situ sequencing through hybrid block coding

作者：Tianyi Chang, Wuji Han, Mengcheng Jiang, Jizhou Li, Zhizhao Liao, Mingchuan Tang, Jianyun Zhang, J. Shen, Zitian Chen, Peng Fei, Xianwen Ren, Yuhong Pang, Guanbo Wang, Jianbin Wang, Yanyi Huang · 发表于：Proceedings of the National Academy of Sciences · 年份：2023 · DOI：10.1073/pnas.2309227120 · 被引用次数：17 · 研究领域：Single-cell and spatial transcriptomics、Gene Regulatory Network Analysis、Gene expression and cancer classification

Spatial transcriptomics technology has revolutionized our understanding of cell types and tissue organization, opening possibilities for researchers to explore transcript distributions at subcellular levels. However, existing methods have limitations in resolution, sensitivity, or speed. To overcome these challenges, we introduce SPRINTseq (Spatially Resolved and signal-diluted Next-generation Targeted sequencing), an innovative in situ sequencing strategy that combines hybrid block coding and molecular dilution strategies. Our method enables fast and sensitive high-resolution data acquisition, as demonstrated by recovering over 142 million transcripts using a 108-gene panel from 453,843 cells from four mouse brain coronal slices in less than 2 d. Using this advanced technology, we uncover the cellular and subcellular molecular architecture of Alzheimer's disease, providing additional information into abnormal cellular behaviors and their subcellular mRNA distribution. This improved spatial transcriptomics technology holds great promise for exploring complex biological processes and disease mechanisms.