Location Location Location! An Evaluation of Spatial Transcriptomics Methods Using Embryonic Chick Tissue

摘要

The spatial organization of cells within a given tissue plays a crucial role in determining their overall function. Driven by the importance of understanding this organization, spatial transcriptomics is quickly coming to the forefront of new Next Generation Sequencing (NGS) applications with the ability to map cellular gene expression back to a specific location within the tissue. To address the growing interest in this area of research, embryonic chick trunk tissue was used to conduct a comparison of two spatial transcriptomic solutions as we aim to determine the capabilities of each and how they might benefit the research at our Institute. The first method of this evaluation, Slide-seq, was published in Science by Macosko et al. This approach uses a 'puck' coated with barcoded beads in known positions at 10um resolution to capture the spatial information of mRNA from a given tissue section placed on the puck. The second method in the comparison is a commercialized kit from 10X Genomics called Visium. In this approach, the spatial information of mRNA from a given tissue section is obtained using 55um barcoded spots in known positions within a designated 'capture area' on a special microscope slide. The Visium solution also uses H&E staining and brightfield imaging of the tissue to inform the 10X Genomics Space Ranger analysis software tool following sequencing. Both methods require fresh frozen tissue sections at 10um thickness, use poly(dT) to capture mRNA transcripts for cDNA synthesis, and construct NGS libraries that utilize Illumina sequencing platforms to deliver unbiased spatial analysis. A 10X Genomics 3' Single Cell RNA-seq dataset was also generated from the embryonic chick trunk tissue to inform and assist the analysis of both methods. Here we present our assessment of the two spatial methods and the challenges we faced in this pilot.