By Sang Ho Kwon.
Recent advancements in spatially-resolved transcriptomics (SRT) technologies have ushered in a new era of possibilities for biological research. These technologies offer the unique ability to map biomolecular information within the native tissue architecture. Preserving the spatial resolution of genome-wide gene expression allows researchers to obtain a more holistic view of the tissue microenvironment, particularly the underlying molecular and cellular dynamics in a spatial-anatomical context, which is useful to understand the composition, states, and function of individual cell types, as well as their interactions with one another in a defined microenvironment.
By Nick Eagles
As part of recent LIBD work with spatial gene expression, I recently was recommended the tool Space Ranger, which provides software pipelines walking Visium spatial RNA-seq samples through the steps we ultimately need to explore gene expression coupled with spatial information. In this blog post, I’ll explain how to start using Space Ranger at JHPCE, focusing heavily on the set-up details relevant to this cluster in particular.