JAX Xenium in situ RNA and H&E profiling of normal human lung and skin tissues: A component of the SenNet spatial technology benchmarking project
Year: 2026
Type: other
Abstract: First generation Xenium in situ RNA profiling provides a highly sensitive, sub-cellular and spatially resolved approach to identify targeted RNA transcripts in human tissues. Such high-resolution mapping within intact tissue architecture aids in the identification of cellular senescence, where spatial context is essential for understanding cell–cell interactions. Therefore, this technology was chosen as one of a number of spatial technologies to compare within the SenNet benchmarking project, a project that generates data on human skin and lung samples, all derived from the same 5 donors, across multiple technologies. Two (JAX & Mt Sinai) Tissue Mapping Centers generated Xenium data utilizing the same 371 gene custom Xenium probe panel in addition to utilizing the 10x Genomics Segmentation kit enabling cell segmentation utilizing DAPI staining for nuclei detection and immunofluorescence detection of cell membranes (a single channel with ATP1A1, CD45, and E-cadherin antibodies), cytoplasmic RNA (18S Ribosomal RNA), and, for some cells, an interior protein stain (alphaSMA/Vimentin antibodies). In this collection are the data generated from the JAX Tissue Mapping Center which includes post-Xenium hematoxylin and eosin (H&E) staining. The H&E staining provides essential histological context, enabling the correlation of spatial transcriptomics data with tissue morphology. We aim to correlate spatial patterns of senescent cells with structural features or pathological changes in tissue morphology. Moreover, H&E staining facilitates cross-study benchmarking by offering a standardized morphological reference, allowing different research groups to compare tissue integrity, staining quality, and anatomical landmarks across experiments.
Institutions: Jackson Laboratory, UConn Health
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7163910296