Spatial Biology and Genomics Core Equipment and Services
Akoya Biosciences PhenoCycler
PhenoCycler-Fusion 2.0
The PhenoCycler Fusion imaging system is a high-plex spatial proteomics platform capable of interrogating 100+ biomarkers at sub-cellular resolution on whole tissue slides, fresh frozen or FFPE.
The technology relies on a single staining step using antibodies conjugated to unique oligo barcodes. The stained tissue is loaded on the platform, where microfluidics and imaging modules sequentially introduce and image fluorescent reporter oligos, three at a time. The single .QPTIFF output file provides a detailed representation of tissue architecture, cell morphology, phenotype, and spatial relationships, which can be visualized and analyzed by open-source software tools.
The Spatial Biology and Genomics (SBG) Core has developed a Human Immune Microenvironment Panel for use with the system. Our scientists can assist you in further customizing this panel or can even design a whole new panel to fit your project’s needs.
PhenoImager Fusion
The PhenoImager Fusion system is a high-speed brightfield and fluorescent whole-slide imaging platform. It utilizes multispectral imaging technology for the detection and measurement of up to six markers at a time, thereby offering a high-throughput solution for biomarker discovery and validation. The PhenoImager Fusion system is compatible with Opal Dye Reagents and Kits.
Learn more about the Akoya system
SBG Core – Akoya Bioscience Flyer
Spatial Genomics – GenePS System
The GenePS spatial platform uses Sequential fluorescence in situ hybridization (seqFISH) and makes it easy to image and decode complex molecular identities and locations directly within single cells and intact tissue microenvironments. The GenePS system enables multiplexed single-cell analyses of RNA, DNA, and protein beyond the capabilities of other types of spatial analyses. This technology can reveal thousands of biomolecules in single cells while maintaining spatial tissue organization. The GenePS system can assay single-cell gene expression, protein expression, genomic, and epigenomic states, thus allowing identification of cell types and elucidation of their roles in cellular neighborhoods and microenvironments.
Off-the-shelf and custom gene panels are available to meet your project needs and powerful analysis software allows you to quickly review the results.
Learn more about the GenePS system
10X Genomics Chromium X – Single Cell Technology
The Chromium X harnesses the power of microfluidics to automate single cell partitioning in a fast, efficient and reliable manner.
GEM-X Universal 3’ Gene Expression v4
Probe the entire transcriptome at single cell resolution to distinguish cell types and molecular states of biological samples. Gene expression can be combined with detection of hundreds of cell surface proteins to enable higher parameter analysis. The GEM-X technology provides high sensitivity to find rare transcripts even in cells with low RNA content.
GEM-X Universal 5’ Gene Expression v3 (immune profiling option)
Enables simultaneously profiling of gene expression and immune repertoire (BCR/TCR) from the same cell to correlate clonotype with the corresponding cell subtype. Full-length receptor sequencing can be done on T cells or B cells to provide functional data.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
Combines gene expression analysis with ATAC seq on the same cell to provide a snapshot of both transcript data and cellular epigenomic state. Gene regulation analysis is enhanced by linking target genes with open chromatin regions.
Chromium Next GEM Single Cell ATAC Kit v2
Explore cellular epigenetic heterogeneity by profiling open chromatin regions at single nuclei resolution.
GEM-X Flex Gene Expression
The new fix and freeze protocol allows storage and batching of samples for downstream single cell gene expression analysis from a human or mouse transcriptome. This new technique can be applied to bring single cell profiling of FFPE tissue.
Learn more about the 10X Genomics Chromium X System
CyTOF (Helios)
Mass cytometry (Helios, a CyTOF System, Standard Biotools) combines time-of-flight mass spectrometry with metal-labeling technology to enable breakthrough discovery and comprehensive functional profiling applications. With 135 available detection channels, this technology enables you to fully study the functional complexity of biological systems at the single cell level, including phosphoprotein-signaling analysis on subpopulations of cells.
Learn more about Mass Cytometry
Image Mass Cytometry (Hyperion)
Imaging Mass Cytometry (IMC) on the Hyperion Imaging System uniquely combines a precisely directed laser beam focused at 1 μm to collect biological samples stained with metal-tagged Maxpar® antibodies and directs these tags for analysis with proven CyTOF technology. Bringing together the high-multiplex capabilities of mass cytometry with imaging using metal-tagged antibodies allows simultaneous interrogation of 4 to 37 protein markers in tissues and tumors at subcellular resolution while preserving the information in tissue architecture and cell morphology. Now researchers can detect discrete signals from each ionized metal tag based on differences in mass instead of wavelength at 1 Da resolution, and in contrast to fluorescence results, they can achieve uniform staining with minimal background.
The SBG Core has developed a Human Tumor Microenvironment Panel available for use with the IMC. Using this panel as a backbone, the core can customize this panel based on your project’s needs. Our IMC scientists can also assist with designing a whole new targeted panel for your specific project.
Learn more about Image Mass Cytometry
SBG Core Human Tumor Microenvironment Panel
Next Generation Sequencing (NGS)
Using Illumina’s Next Generation Sequencing platform, the SBG Core offers Whole Genome Sequencing (WGS) for DNA, and RNA sequencing for both mRNA and non-coding RNA. Our services include every step of processing (nucleic acid sample isolation, library prep, sequencing, and data analysis). The SBG Core can help determine which service options will fit your project’s needs.
Microbiome Metagenomics
The SBG Core harnesses the power of next generation sequencing to provide Microbiome Metagenomics services. Researchers can investigate microbial communities and individual species in a wide range of sample types. We provide both 16S and whole genome shotgun analysis for your metagenomics needs. Our services include every step of processing (nucleic acid sample isolation, library prep, sequencing and data analysis).
Read about a comparison of 16S and whole genome shotgun metagenomics
Bioinformatics and Data Analysis
Our bioinformatics team provides the latest bioinformatics resources and expertise to deliver meaningful analysis results from data generated on all available ‘omics’ platforms. We have extensive experience with many popular software packages for single-cell spatial omics (DeepCell, Seurat, Qupath, SpatialExperiment) analyses, bulk RNA-seq (RSEM, edgeR, Deseq2), single-cell RNA-seq (cellranger, seurat, scVelo, slingshot, cellchat), metagenomics (QIIME, Kraken, MetaPhlAn2) and mass cytometry (OMIQ). We have access to private Linux servers as well as the USC High Performance Computing Core to tackle any analysis project, regardless of size. We provide a whole suite of services including analysis of experiments performed elsewhere.
