Spatial transcriptomics methods permit gene expression from focal areas within a tissue to be profiled while maintaining the morphologic context of the tissue microenvironment. This presentation will address considerations based on the needs of a study for selecting the best fit to what are new methods still in their infancy. These important considerations start with; i) whether focal profiling will provide data that profiling of bulk tissue will not; ii) is it necessary to profile single cells or are larger focal areas such as single glands sufficient; iii) what is the size of such histologic regions and Is it necessary to have histologically discrete profiling without cross-contamination from adjacent histologic regions or cells; iv) What is the throughput required, just a few sections or lots of sections from 100+ tissues, animals, or subjects, and within each section, how many focal areas; v) Is it desirable to measure splice variants, snRNA, long non-coding RNA, histones - if so, then a 3’ biased assay method would be unsuited for the need vi) What tissue type does the method use, and how does that match up with what the investigator has available - Frfsh frozen, FFPE, H&E stained, antibody-stained; vii) What is the sensitivity – can all the genes measured from a bulk sample, including low expressed ones be measured; viii) What is the dynamic range; i.e. can a broad range of expressed genes from low to high be measured quantitatively at the same time. As methods continue in their development, the choice will also be whether the investigator wants to measure a panel of antigens at the same time as gene expression. If so, can this be from different serial sections, or does it have to be from the same section, same focal area. And of course, there is the question of cost. Different methods will be presented within the context of these questions, and spatial profiling data using TempO-Seq® will be provided to demonstrate several of these considerations. This data will also demonstrate the potential of spatial profiling in understanding the specificity and context of gene expression within the tissue microenvironment.
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