Spatial transcriptomics: Technologies, applications and experimental considerations.
Ye Wang, Bin Liu, Gexin Zhao, YooJin Lee, Anton Buzdin, Xiaofeng Mu, Joseph Zhao, Hong Chen, Xinmin Li
Author Information
Ye Wang: Clinical Laboratory, The Affiliated Qingdao Central Hospital of Medical College of Qingdao University, Qingdao 266042, China. Electronic address: yewang@qdu.edu.cn.
Bin Liu: Departments of Medical Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang 110042, China.
Gexin Zhao: UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA.
YooJin Lee: UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA.
Anton Buzdin: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Moscow Institute of Physics and Technology, Moscow Region, 141701, Russia; World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, Moscow 119991, Russia.
Xiaofeng Mu: Clinical Laboratory, The Affiliated Qingdao Central Hospital of Medical College of Qingdao University, Qingdao 266042, China.
Joseph Zhao: UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA.
Hong Chen: Heilongjiang Academy of Traditional Chinese Medicine, No. 142, Sanfu Street, Xiangfang District, Harbin City, Heilongjiang Province 150036, China.
Xinmin Li: UCLA Technology Center for Genomics & Bioinformatics, Department of Pathology & Laboratory Medicine, 650 Charles E Young Dr., Los Angeles, CA 90095, USA. Electronic address: xinminli@mednet.ucla.edu.
The diverse cell types of an organ have a highly structured organization to enable their efficient and correct function. To fully appreciate gene functions in a given cell type, one needs to understand how much, when and where the gene is expressed. Classic bulk RNA sequencing and popular single cell sequencing destroy cell structural organization and fail to provide spatial information. However, the spatial location of gene expression or of the cell in a complex tissue provides key clues to comprehend how the neighboring genes or cells cross talk, transduce signals and work together as a team to complete the job. The functional requirement for the spatial content has been a driving force for rapid development of the spatial transcriptomics technologies in the past few years. Here, we present an overview of current spatial technologies with a special focus on the commercially available or currently being commercialized technologies, highlight their applications by category and discuss experimental considerations for a first spatial experiment.
