The Research Technologies Branch (RTB), Spatial Technologies Resource provides accessibility, expertise and innovation to utilize spatial transcriptomic and proteomic technologies in support of the Division of Intramural Research (DIR) scientists at both the NIH main campus in Maryland and Rocky Mountain Laboratories in Montana.
The Spatial Technologies Resource provides experimental design, project coordination, sample preparation, data generation and analysis using commercial platforms and novel approaches to facilitate the adoption of these technologies into DIR research. The STR draws upon expertise across several units within the RTB, including but not limited to; Genomics, Proteomics, Imaging, Cytometry, and Data Sciences to develop a spatial approach that integrates well with investigator inquiries and needs.
Major Areas of Support
- Spatial Transcriptomics and Proteomics of tissue sections.
- Whole transcriptome spatial gene expression.
- Panel-based in situ hybridization approaches.
- High-throughput mapping of transcripts at single-cell resolution.
Instrumentation
The Spatial Technologies Resource currently supports two major commercial platforms for spatial interrogation of tissue samples. The 10X Genomics Xenium enables spatial transcript identification and localization at single-cell resolution for up to 5,000 RNA targets using a panel-based in situ hybridization and detection approach. For unbiased surveys and discovery applications, the 10X Genomics Visium HD workflow offers near-single cell resolution with both probe-based whole transcriptome and 3’ gene expression options using the CytAssist instrument.
The Xenium can generate single-cell resolution of spatially mapped transcripts and has built-in cell segmentation approaches.
Xenium data showing the spatial localization of 24 Collagen gene markers (Small dots in various colors) in Mouse lymph node tissue stained with DAPI for nuclei (Blue) and ATP1A|CD45|E-Cadeherin for cell boundaries (Magenta).
The Cytassist is used in conjunction with the Visium HD assay to transfer probes hybridized on tissue sections to an arrayed capture slide.
Access
Currently, collaborating with RTB is only available to federally funded institutions. Researchers may access all RTB support services by visiting RTB on Inside NIAID (this link is only available to NIAID lab scientists).