Equipment
Click here for a full equipment list across all School of Medicine Research Cores
The nCounter Pro Analysis System and the Sprint Profiler provide a cost-effective automated solution for multiplex analysis of up to 800 targets. The simple workflow requires just 15 minutes of hands-on time and produces highly reproducible data, requiring no amplification or technical replicates.
The panels cover different areas of research, such as Oncology, Immunology, Cardiovascular Diseases, Cell & Gene Therapy, Stem Cells, Regenerative Medicine, Infections Disease, Neuroscience, etc.
Customizing panels is another available tool. It is possible to include different targets in the chosen panel or customize your panel.
nCounter can be a shift option in studies that use the PCR technique, eliminating primer design and validation steps and optimizing the use of biological samples without technical replicates.
The nCounter technology requires no amplification or cDNA synthesis.
Analyzes can be performed using nSolver or Rosalinda software, both online platforms. Both software is easy to use, generating high throughput data and publishable pictures in less than 1 hour.
More information:
Whole transcriptome spatial discovery in a single-cell scale.
Visium HD Spatial Gene Expression slides contain two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides arrayed in ~11 million 2 x 2 μm barcoded squares without gaps, achieving single–cell–scale spatial resolution.
More information:
If you have an interest or want to know more about this platform, please contact Dr Ana de Oliveira at ak4yj@virginia.edu
CosMxTM Spatial Molecular Imager (SMI) is the first high-plex in situ analysis platform to provide spatial multi-omics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of 1,000 or 6,000 RNA and 64 or 120 proteins at the same time. It is the flexible, spatial single-cell imaging platform that will drive deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery.
The CosMxTM SMI platform is an integrated system with mature cyclic in situ hybridization chemistry, an ultra-high-resolution imaging readout instrument, and interactive data analysis and visualization software.
| CosMx SMI – System Specifications | |
| Resolution | Subcellular resolution (<100nnm) |
| Throughput | Up to 1 million cells/sample, 4 samples/run
Up to 16slides/week |
| Tissue Compatibility | FFPE, Fresh Frozen, Organoids, Culture Cell |
| Multiplexing capability (option to customize) |
|
| Flexible scan area | Up to 100mm2 |
| Flexible scan area | Includes instrumentation, validated panels and reagents, cloud data storage and analysis |
CosMx SMI Workflow
- A 5μm FFPE or fresh frozen tissue section is fixed and permeabilized.
- RNA probes are hybridized to their targets in the tissue sample.
- The tissue sample is washed, then incubated with oligo-labeled antibodies for morphology marker staining.
- After washing, the flow cell is assembled and loaded onto the SMI instrument for morphology marker imaging.
- The desired imaging area(s) on the tissue (up to 100 mm2) are selected.
- The instrument automates rounds of reporter binding and fluorescent imaging to read out the barcodes on each imaged RNA probe or protein antibody.
More information:
CosMx 1000-plex Human Panel (Excel)
AtoMx. Spatial Informatics Platform (PDF)
IsoCode Chip – Single-Cell Analysis
Isoplexis is a multiplex phenotyping analysis that allows complete functional characterization of a single-cell.
Cells are initially stained (2 markers) and captured individually in the chip’s microchambers. Over 30 cytokines, chemokines, and a full range of phosphoproteins are monitored for 20 hours.
Panel List:
Single-Cell Secretome
Human Adaptive Immune
Granzyme B, IFN-γ, MIP-1α, Perforin, TNF-α, TNF-β, GM-CSF, IL-2, IL-5, IL-7, IL-8, IL-9, IL-12, IL-15, IL-21, CCL11, IP-10, MIP-1β, RANTES, IL-4, IL-10, IL-13, IL-22, TGFβ1, sCD137, sCD40L, IL-1β, IL-6, IL-17A, IL-17F, MCP-1, MCP-4
Human Natural Killer
Granzyme B, IFN-γ, MIP-1α, Perforin, TNF-α, TNF-β, GM-CSF, IL-2, IL-5, IL-7, IL-8, IL-9, IL-12, IL-15, IL-21, CCL11, IP-10, MIP-1β, RANTES, IL-4, IL-10, IL-13, IL-22, TGFβ1, sCD137, sCD40L, IL-1β, IL-6, IL-17A, IL-17F, MCP-1, MCP-4
Human Innate Immune
IFN-γ, MIP-1α, TNF-α, TNF-β, GM-CSF, IL-8, IL-9, IL-15, IL-18, TGF-α, IL-5, CCL11, IP-10, MIP-1β, RANTES, BCA-1, IL-10, IL-13, IL-22, sCD40L, IL-1β, IL-6, IL-12-p40, IL-12, IL-17A, IL-17F, MCP-1, MCP-4, MIF, EGF, PDGF-BB, VEGF
Human Inflammation
GM-CSF, IFN-γ, IL-2, IL-12, TNF-α, TNF-β, IL-4, IL-5, IL-7, IL-9, IL-13, CCL11, IL-8, IP-10, MCP-1, MCP-4, MIP-1α, MIP-1β, RANTES, IL-10, IL-15, IL-22, TGF-β1, IL-1β, IL-6, IL-17A, IL-17F, IL-21, Granzyme B, Perforin, sCD40L, sCD137
Non-human Primate Adaptive Immune
TNF-α, MCP-1, IL-2, IL-4, MIP-1β, IL-6, IL-8, IL-1β, RANTES, IFN-g, IP-10, MIP-1α, MIF, GM-CSF
Mouse Adaptive Immune
Granzyme B, IFN-γ, MIP-1α, TNF-α, GM-CSF, IL-2, IL-5, IL-7, IL-12p70, IL-15, IL-21, sCD137, CCL11, CXCL1, CXCL13, IP-10, RANTES, Fas, IL-4, IL-10, IL-13, IL-27, TGFβ1, IL-6, IL-17A, MCP-1, IL-1β
Mouse Innate Immune
IFN-γ, TNF-a, MIP-1a, IL-15, GM-CSF, IL-5, IL-10, IL-13, IL-6, IL-17A, MCP-1, IP-10, MIP-1b, EGF, PDGF-BB, MIF
Single-Cell Intracellular PhosphoProteome
Human Tumor Signaling
P-PRAS40, P-IkBα, P-NF-kβ p65, P-Met, P-p44/42 MAPK, P-S6 Ribosomal, P-p90RSK, P-STAT3, P-MEK1/2, P-Stat1, P-Stat5, P-eIF4E, Cleaved PARP*, Alpha Tubulin
CodePlex Chip – Secretome Analysis in Supernatant or Biological Fluid
- Completely automated workflow
- 5.5 uL per sample in duplicate
- Measure more than 30 cytokines in bulk
- Run 8 samples per Chip
- Modular, load 8-32 samples per run
- Limit of detection: 5-5000 pg/ml
Panel List
Human Adaptive Immune
GM-CSF, Granzyme B, IFN-γ, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-13, IL-15, IL-17A, IP-10, MCP-1, MIP-1α, MIP-1β, Perforin, sCD137, TNF-α, TNF-β
Human Innate Immune
EGF, GM-CSF, Granzyme B, IFN-γ, IL-1β, IL-4, IL-6, IL-7, IL-8, IL-10, IL-15, IP-10, MCP-1, MIP-1α, MIP-1β, PDGF-BB, sCD137, TNF-α, VEGF
Human Cytokine Storm
GM-CSF, IFN-γ, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-13, IL-17A, IP-10, MCP-1, MIP-1α, MIP-1β, Perforin, TNF-α
Human Stem Cell Signaling
IL-17A, MIP-1α, IL-6, IL-4, MIP-1β, IL-8, IFN-γ, GM-CSF, IL-10, TNF-α, MCP-1, IL-2, IL-15, RANTES, IL-1α, IL-1β, CXCL5
Human Cancer Signaling
EGF, IFN-γ, IL-1α, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-13, MCP-1, MIF, PDGF-BB, RANTES, TNF-α
Mouse Adaptive Immune
GM-CSF, IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-17A, IP-10, KC, MCP-1, MIP-1α, RANTES, TNF-α
Mouse Innate Immune
IFN-γ, TNF-α, MIP-1α, IL-15, GM-CSF, IL-5, IL-10, IL-13, IL-6, IL-17A, MCP-1, IP-10, MIP-1β, EGF, PDGF-BB, MIF
Mouse Inflammation
IFN-γ, TNF-α, MIP-1α, IL-2, IL-5, IL-10, IL-13, IL-4, IL-6, IL-1β, IL-17A, IL-12, MCP-1, IP-10, KC, GM-CSF
Non-human Primate Adaptive Immune
GM-CSF, IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-8, IP-10, MCP-1, MIP-1α, MIP-1β, RANTES, TNF-α
Mouse Cancer Signaling – in pipeline
EGF, IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-10, IL-13, MCP-1, MIF, PDGF-BB, RANTES, TNF-α, VEGF
Mouse Stem Cell Signaling – in pipeline
GM-CSF, IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-10, IL-15, IL-17A, MCP-1, MIP-1α, MIP-1β, RANTES, TNF-α
Human Tumor Signaling – in pipeline
P-PRAS40, P-IkBα, P-NF-kβ p65, P-Met, P-p44/42 MAPK, P-S6 Ribosomal, P-Rb, P-p90RSK, P-STAT3, P-MEK1/2, P-Stat1, P-Stat5, P-eIF4E, Cleaved PARP, Alpha Tubulin
More information:
Isoplexis-IsoCode-SingleCellAnalysis
Isoplexis-CodePLex-HighPlex-Immunoassssay
Website
Tissue Imaging Mass Cytometry
The Hyperion XTi is a multiplexed tissue imager that uses metal-tagged antibodies, instead of fluorophores, to simultaneously and reliably acquire 40-plus protein and RNA markers, without autofluorescence interference. 40-plus markers can be visualized in real time without the need of multiple acquisition cycles.
More Information
The Hyperion XTi was purchased in collaboration with the Flow Cytometry Core Facility using Cancer Center Funding
The high throughput microplate imager for high-content analysis.
Cell Analysis
- Fixed-Cell Assays
- Live-Cell Assays
- (CO2 and Temperature Control)
- Spheroids and Organoids
Resolution Features
- Confocal
- Non-Confocal
- Fluorescence
- Brightfield
- Digital Phase Contrast Images
Dry Objective
- 1.25x
- 5.0x
- 10.0x
Water Objective
- 20x
- 40x
- 63x
8 LEDs Excite
- 365
- 405
- 440
- 475
- 510
- 550
- 630
- 680
Application
- Cell Counting
- Live / Dead Cell Counting
- Nuclear Analysis
- Nuclei Counting
- Marker. Quantification
- Cytosol to Nucleus Translocation
- Cytosol to Membrane Translocation
- Receptor Internalization
- Fluorescence resonance energy transfer (FRET)
- Cell Cycle
- Cell Shape
- Phenotype Classification
- Migration
- Cell Division
- 3D Analysis – Spheroid
More information:
Operetta-Solutions-for-3D-Cell-Cultures
Plate your cells, image your cells, choose your best cells, and isolate them all on one consumable. The CellRaft increases the viability and results in less perturbed phenotypes, compared to traditional methods.
More Information
The Stem Cell Lab is available again
Facilities:
Appropriate facilities for the development of iPSC and organoid culture.
All instrumentation available:
- 02 Hoods in the regular lab room
- 01 Hood in the quarantine room
- HERA Cell Vios 160i CO2 Incubator (04 incubators)
- EVOS XL Core microscope inside the hood (magnification 4x, 10x, 20x, 40x)
- EVOS FLc with for color filters (Cy5, GFP, DAPI, TxRed) and 4 magnifications
- Cell counting
- Water bath
- Centrifuge
- Sonic Dismembrator Model 500 – Fisher Scientific
- Refrigerator, -20ºC Freezer and -80ºC Freezer
Scientific support
Training support
Cell maintenance
Mycoplasma control (screening with Lonza kit)
