Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

Renjie Liao; Defeng Fu; Zaoxu Xu; Han Liang; Xiaoran Zhou; Yiling Elaine Chen; Xue‐Qi Liu; Ji Cheng; Ruidong Guo; Li Chen; Huihua Xia; Gailing Li; Diewen Feng; Wei Chen; Yang Chen; Longchao Chen; Zihang Huang; Yang Zhou; Qingbin Chen; Dexia Chen; Shuguang Xuan; Changling Zhang; Yongyi Lu; Hui Wang; Taiqing Feng; Yuanye Bao; Luyang Zhao; Erkai Liu; Gufeng Wang

doi:10.1101/2025.01.15.633111

Molecular BiologybioRxivJan 15, 2025

Preprint

Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

Renjie Liao, Defeng Fu, Zaoxu Xu iD, Han Liang, Xiaoran Zhou iD, Yiling Elaine Chen iD, Xue‐Qi Liu iD, Ji Cheng iD, Ruidong Guo, Li Chen iD, Huihua Xia, Gailing Li iD, Diewen Feng, Wei Chen iD, Yang Chen iD, Longchao Chen, Zihang Huang iD, Yang Zhou, Qingbin Chen iD, Dexia Chen, Shuguang Xuan iD, Changling Zhang, Yongyi Lu, Hui Wang iD, Taiqing Feng, , Gufeng Wang iD

Abstract

The advent of spatial transcriptomics has dramatically expanded our ability to study the vast network of cell-cell interactions at the molecular level in tissue. Among current methods, sequencing-based approaches have great potential in discovering because of its unbiased capture. In the last couple of years, the spatial resolution for the capture addresses has been significantly improved from 100 m to <1 m, well below the size of a mammalian cell. However, the capture efficiency has always been a pain point, [~]one order of magnitude lower than that of single cell RNA sequencing (scRNA-seq). The low capture efficiency limits the depth and breadth of its applications in the study of complex biological systems and diseases. Here, we introduce Salus Spatial transcriptomic system (Salus-STS), which provides [~]1 m capture resolution and a capture efficiency [~]1 order of magnitude higher than other current methods. Analysis with sub-cellular resolution becomes practical for sequencing-based spatial transcriptomics.

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