Biophysical development of single-cell spatial transcriptome data analysis visualization platform

[ Instrument Network Instrument Development ] Single-cell sequencing technology is a technique for high-throughput sequencing analysis of genomes, transcriptomes, and epigenetic groups at the single-cell level. Single-cell sequencing technology can reveal intercellular heterogeneity at the omics level. The single-cell level cell lineage tracking technology ranks first among the top 10 scientific breakthroughs in the 2018 Science magazine. Conventional single-cell transcriptome sequencing technology loses spatial location information critical to the cell in the original tissue, while single-cell spatial transcriptome technology preserves and records spatial location information of cells while performing single-cell transcriptome sequencing. Spatial transcriptome technology can reveal the interaction between cells and the microenvironment in which cells are located. It will become a research tool in the fields of developmental biology, neurobiology, immunobiology, and tumor microenvironment.

On November 12th, Nucleic Acids Research published a paper on the high-throughput sequencing center of the Institute of Biophysics of the Chinese Academy of Sciences entitled SpatialDB: a database for spatially resolved transcriptomes, releasing the first single-cell spatial transcriptome. Database and data online visualization platform. The SpatialDB system includes data from eight spatial transcriptome technologies from five species, establishes a spatial transcriptome data analysis process, and realizes online visualization of spatial transcriptome data, while providing spatially differentially expressed genes and their functional richness. Set the comments for the analysis.

Academician of the Chinese Academy of Sciences, researcher Chen Runsheng of the Institute of Biophysics, and senior engineer Chen Xiaowei are co-authors of the paper. Fan Zhen, senior engineer of the High-throughput Sequencing Center of Biophysics, is the first author of the paper. The research was funded by the Chinese Academy of Sciences key technical talent project, the National Natural Science Foundation and national key research and development projects.