Spatial Biology

The Akoya PhenoCycler Fusion 2.0 spatial biology platform provides the highly multiplexed immunofluorescent detection of up to 60 protein biomarkers in a single tissue section mounted on a standard microscope slide. The PhenoCycler Fusion employs the Co-detection by indexing (CODEX) technology, whereby antibodies conjugated to unique DNA sequences simultaneously label a tissue section. The unique DNA barcodes bound to the antibodies are then detected using a complementary DNA reporter probe labeled with a fluorescent dye. The antibodies bound to the tissue section can be detected cyclically through the binding of a reporter probe to the barcode, imaging of the tissue section and then eluting and washing away the reporter. This procedure can then be repeated until all antibodies bound to the tissue section have been detected. Antibodies labeled by Akoya Biosciences are available for use on the Akoya PhenoCycler Fusion for mouse and human fresh frozen and formalin fixed paraffin embedded (FFPE) tissues. The Cellular Imaging and Histology Core has developed a 26-antibody immune cell phenotyping panel for use in FFPE mouse tissue samples. The Core facility staff can also assist in the custom barcoding of any antibody required for your specific research project.

The Akoya PhenoCycler Fusion 2.0 system was acquired using funding provided by an S10 Shared Instrumentation Grant award from the National Institute of Health. If you are publishing data acquired using the Akoya PhenoCycler Fusion 2.0, please reference the S10 grant award S10OD032377.

Additional information on the PhenoCycler Fusion 2.0 can be found at the Akoya Biosciences website: https://www.akoyabio.com/

The 10x Genomics Xenium Analyzer provides ultra-high-plex in situ detection of RNA molecules at subcellular resolution on tissue sections mounted on microscopic slides. 10x Genomics provides several curated gene panels for the detection of RNA transcripts in human and mouse tissues, in addition to providing the option for the creation of fully custom standalone panels. 10x Genomics also provides several assays for the Xenium Analyzer including Xenium v1 for the detection of <500 genes, Xenium Prime for the detection of over 5000 genes and Xenium Protein subpanels for the detection of select proteins. Optional cell segmentation staining provides resulting data with high confidence, single cell resolution. The Xenium Analyzer includes intuitive on-board software for data analysis and 10x Genomics provides the Xenium Explorer software for interactive data visualization.

Additional Information of the Xenium Analyzer can be found at the 10x Genomics website: https://www.10xgenomics.com/platforms/xenium

The Cellular Imaging and Histology Core houses a 10x Genomics CytAssist instrument to aid in Visium HD sequencing based spatial transcriptomics workflow. The Visium HD assay combines histology and spatially resolved whole transcriptome gene expression profiling to localize and quantify gene expression within the tissue context. It is compatible with formalin fixed paraffin embedded (FFPE) and fresh frozen tissues. Visium HD Spatial Gene Expression slides contain two 6.5 x 6.5 mm capture areas with a continuous lawn of oligonucleotides arrayed into ~11 million 2 x 2 µm barcoded squares. The construction of the Visium libraries and the Illumina sequencing is performed in collaboration with the Rutgers NJMS Genomics Center: https://research.njms.rutgers.edu/genomics/

Additional information on the Visium HD platform and the CytAssist instrument can be found at the 10x Genomics website: https://www.10xgenomics.com/platforms/visium