The Yale Undergraduate Research Journal


Spatial transcriptomics is an emerging approach which characterizes gene expression profiles for a more nuanced understanding of biological processes at a tissue level. This offers significant advantages over traditional omics which require the digestion of tissues and subsequent isolation of cells, during which the spatial information is completely lost. Lymph nodes are an integral part of the immune system and an in-depth analysis of its spatial organization will provide useful insights which can be applicable in the development of novel immunotherapies. In this study, the mouse lymph node is characterized using the newly developed microfluidic-based approach, Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq). Unsupervised spatial clustering analysis via the Seurat R package yielded 8 unique clusters, 3 of which were identified as lymphatic muscle cells, macrophages and T and NK cells, respectively. SpatialDE and GO analysis further elucidated the biological processes associated with the patterns of gene expression.