Protocol to decipher complex spatial transcriptomics data using STMiner

STAR Protocols, vol. 6, pp. 103838

Abstract

Complex spatial transcriptomics (ST) data analysis can be challenging due to uneven sampling, sparsity, and ambiguous tissue boundaries. Here, we present a protocol for deciphering complex ST data using STMiner. We describe steps for installing STMiner, loading ST data into STMiner, and identifying spatially variable genes. We then detail procedures for determining gene sets associated with the structure of interest and obtaining spatial expression patterns. This protocol can be applied to varying resolutions and platforms, without additional reference data. For complete details on the use and execution of this protocol, please refer to Sun et al. 1

Authors 3

1. Peisen Sun corresponding

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China. Electronic address: sunpeisen@stu.xjtu.edu.cn

2. Mingxuan Li

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China

3. Kai Ye corresponding Aachen

   Leiden University · Xi'an Jiaotong University · First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; Department of Gynecology and Obstetrics, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Faculty of Science, Leiden University, Leiden, the Netherlands. Electronic address: kaiye@xjtu.edu.cn