Your One-Stop Shop

The Spatial Technologies Unit is proud to carry almost every instrument and assay available in the field. From single cell to spatial, we have options for every type of sample and study. The Unit can acomodate all study sizes, from small pilots to clinical trials and population level projects. No matter your research question, we have a solution for you.

From grant applications and study design to final analyzed data, all of our assays are performed in-house by a team of experts who follow your project from start to finish.

If you are unsure of what assay will benefit your research the most, our experts are available to assist you. Just schedule a consultation with us via the contact link.

Our Services

10x Genomics Single Cell/Nuclei

The STU provides fully automated and manual single cell and nucleus sequencing services, including immunoprofiling (VDJ sequencing), cellular indexing of transcriptomes and epitopes (CITE-Seq), and fixed RNA profiling. Single Cell/Nucleus services include:

  • Tissue preparation and dissociation (optional).
  • Single Cell/Nuclei Suspension Preparation (optional).
  • Library preparation and sequencing.
  • Cell Ranger output.
  • Downstream analysis (optional).

For assistance selecting the best assay for your project, schedule a consultation with us, or access the 10x assay selector.

Single Cell Gene Expression
Description Species Compatibility Sample Compatibility Workflow Options Throughput
Reverse transcription-based 3′ or 5′ whole transcriptome gene expression. Species non-specific. Fresh cells or nuclei. Sample multiplexing, Automation. Up to 320,000 cells per run.
Single Cell Immunoprofiling
Description Species Compatibility Sample Compatibility Workflow Options Throughput
Analysis of TCR/BCR sequencing, combined 5’ gene expression. Human and mouse. Fresh cells or nuclei. Automation. Up to 320,000 cells per run.
Fixed RNA Profiling
Description Species Compatibility Sample Compatibility Workflow Options Throughput
Probe-based, whole transcriptome 3′ gene expression. Human and mouse. Fresh or fixed cells or nuclei (FFPE). Built-in Multiplexing Up to 1M cells per run.
Single Cell CITE-Seq
Description Species Compatibility Sample Compatibility Workflow Options Throughput
5’ gene expression with feature barcoding. Species non-specific. Fresh cells or nuclei. Automation. Up to 320,000 cells per run.
Chromium Connect

The 10x Genomics Connect addresses the variability of single cell/nucleus preps by automating the complete process from cell/nucleus suspensions to libraries.

  • Generate consistent results: Reduce single cell data variability, generating reproducible and consistent results.
  • Characterize single cells by gene expression or immune receptor profiling.
  • From sample to sequencing-ready libraries in one day
  • Fast turnaround time and maximal consistency to all 10x genomics single cell assays: single nucleus sequencing, single cell sequencing, gene expression + TCR/BCR profiling (VDJ sequencing), and more!

See how the 10x Genomics Connect maximizes single cell robustness and reproducibility https://support.10xgenomics.com/single-cell-gene-expression/index/doc/technical-note-chromium-connect-consistent-automated-single-cell-gene-expression-library-generation

Please follow this link for more information on the instrument: https://www.10xgenomics.com/instruments/chromium-connect

10x Genomics Single Cell

10x Genomics Visium

The 10x Genomics Visium enables hybridization capture of tissue RNA on slides at up to single cell resolution. Visium generates whole transcriptome libraries which are overlapped with high resolution H&E images at a 1-10 cell resolution depending on tissue type. 

  • Compatible with fresh frozen and FFPE tissue. 
  • Combine whole transcriptome spatial analysis with immunofluorescence protein detection. 
  • Allows for addition of extra probes for specific applications. 

For more information about the assay: https://www.10xgenomics.com/platforms/visium 

The STU offers all versions of the Visium Assay currently supported by 10x Genomics: 

Spatial Gene Expression for Fresh Frozen – Direct Placement Visium:
  • Fresh Frozen only. 
  • Species non-specific – unbiased polyA tail capture. 
  • Slides have either two or four capture areas of 6.5X6.5mm each. 
  • Samples must be mounted directly onto Visium slide. 
  • 55-micron barcoded spots
CytAssist Enabeled Workflow:
  • The starting sample is mounted in a standard pathology slide. 
  • Slides have two capture areas of either 6.5X6.5mm or 11X11mm each. 
  • Compatible with Fresh Frozen and FFPE tissue. 
  • Compatible with human and mouse tissue only. 
  • 55-micron barcoded spots. 
Visium HD
  • 2-micron barcoded spots – single cell resolution. 
  • CytAssist Enabeled. 
  • Slides have two capture areas of 6.5X6.5mm each. 
10x Genomics Visium

10x Xenium

The 10x Genomics Xenium is an in-situ hybridization-based imaging assay that enables high-throughput subcellular mapping of 100s to 1,000s of RNA targets in addition to multiplexed protein on tissue slides. 

  • Over 200mm2 imageable area per slide. 
  • Compatible with Fresh Frozen and FFPE tissue. 
  • Compatible with post-run H&E, Immunofluorescence Staining, and 10X Visium on the same section. 
  • Two slides per instrument run. 
  • Pre-designed, add-on, and standalone custom panels. 

 

Please follow this link for more information on the instrument: https://www.10xgenomics.com/xenium/ 

10x Genomics Xenium

Akoya PhenoCycler-Fusion

The PhenoCycler-Fusion enables multidimensional antibody capture in large tissue sections (>1cm2)

  • Up to 65+ antibodies imaged per slide at single cell resolution
  • Create custom antibody panels for frozen tissue sections and FFPE
  • Characterize in-depth cellular populations without requiring sequencing
  • Ability to work on protein level, capturing intracellular and surface protein markers

Please follow this link for more information: https://www.akoyabio.com/phenocycler/

Akoya PhenoCycler-Fusion (PCF) Services include:

  1. Consultation on the selection of markers using single cell and spatial data.
  2. Design and generation of a custom panel + staining + data generation on the PCF.
  3. Scanning of an already stained stained slide with PCF-compatible panel.
  4. Analysis using the Akoya PCF software.
  5. Downstream analyses (optional).

Akoya PhenoImager HT

State of the art multispectral imaging enables the identification and downstream quantification of multiple overlapping biomarkers (up to 8) without the interference of autofluorescence as the signals are unmixed from one another.

MOTiF™ technology generates unmixed whole slide scans at 40x magnification of up to 7 colors in about 20 minutes (15 x 15 mm region) for analysis of biology across the entire slide in a streamlined workflow and without selection bias.

High speed, low-cost per slide, enabling screening of whole cohorts in a fraction of the cost and time.

Ability to work on protein level, capturing intracellular and surface protein markers.

For more information: https://www.akoyabio.com/phenoimager/instruments/phenoimager-ht/

Akoya PhenoImager HT Services include:

  1. Automated staining on the Leica Bond Rx to minimize variability using an existing antibody panel.
  2. Design and generation of a custom panel + staining on the Leica Bond Rx + scanning on the Polaris.
  3. Scanning of already stained stained slides using fluorescence
  4. Analysis using the Akoya InForm software, enabling minimization of autofluorescence and optimal channel demultiplexing.
  5. Downstream analyses (optional).
Akoya Proteomics

Bruker Vutara VXL

The Vutara VXL comprehensive biological workstation for nanoscale biological imaging enables super-resolution single-molecule localization microscopy (SMLM) technology in a streamlined system with compact footprint. The system enables research on DNA, RNA and proteins, from macromolecular complexes and super-structures, to chromatin structure and chromosomal substructures, to studying functional relationships in genomes and in various subcellular organelles. It supports advanced spatial biology research in extracellular matrix structures, extracellular vesicles (EV), virology, neuroscience, and live-cell imaging. It is combined with Bruker’s microscope fluidics unit, Vutara VXL enables multiplexed imaging for targeted, sub-micrometer multiomics in genomics, transcriptomics, and proteomics research.

  • Achieves depths of >30 μm imaging with proprietary biplane technology.
  • Provides easy yet unlimited multiplexed imaging for spatial genomics, transcriptomics, and proteomics.
  • Proprietary biplane technology, combined with a spatial filter in the emission light path, allows you to acquire 3D data with every acquisition. For thicker specimens, the Vutara allows you to easily perform a Z series and automatically localizes and reconstructs the entire volume.
  • Making cultured cells, cell colonies, tissue sections, and entire model organisms accessible for single-molecule localization experiments.
  • The  platform with SRX software is  also capable of performing ORCA (Optical Reconstruction of Chromatin Architecture)

Please follow this link for further information https://www.bruker.com/en/products-and-solutions/fluorescence-microscopy/super-resolution-microscopes/vutara-vxl.html

Currently our services on the Vutara VXL include:

  • Support for the design and application of a custom experiment, from live cell and tissue imaging to spatial and ORCA.
  • Imaging and analysis of already prepared samples (without any processing or oligoPaint, etc).
Bruker Vutara VXL

NanoString GeoMx DSP

The NanoString GeoMx is a versatile platform enabling spatial transcriptomics and/or spatial proteomics (via barcoded antibodies) on selected regions of interest.

  • Select up to 90 regions of interest (ROI) per tissue slide
  • Ability to work seamlessly with FFPE or frozen tissue sections
  • >18,000 genes quantified per ROI or >100 protein targets
  • Ability to expand and include any target

For more information please visit: https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/

Our services on the GeoMx platform include:

  • Tissue pre-processing (FFPE or frozen) for DSP analysis
  • Tissue stains (4-plex antibody stains and/or additional stains on serial tissue sections) for ROI selections.
  • ROI selection performed by our experts or consultation for selection by the researcher team
  • Various kits are supported inlcluding the WTA (18,000+ genes quantified per region, the CTA 1,000+ genes quantified per ROI, and proteomics assays).
  • Up to 90 ROIs per slide
  • Full service (pre-processing, staining, ROI selection, data generation, data processing (optional)
  • Downstream investigations (optional)
NanoString GeoMx

Vizgen MERSCOPE

The STU is thrilled to host the very first MERSCOPE to leave the Vizgen factory. It offers sub-cellular resolution and high plexity (up to 500 targets) for large areas (~1cm2), corresponding to hundreds of thousands of cells. The high resolution renders it optimal for CNS tissue evaluation.Massively multiplexed, error-robust, single-cell in situ transcriptomic imaging
Quantify and localize RNAs in any tissue sample easily, efficiently, and accurately
Detect low expressing genes that can be missed using other technologies.
Localize RNA transcripts at a subcellular level with ≤100 nm resolution.
High multiplexing with custom gene panel design. Current chemistry up to 500 genes.
Measure your specified genes on many sample or tissue types.


For more information please visit: https://vizgen.com/products/

The current services include:

  • Tissue preparation (frozen or high quality FFPE) and testing for use in the MERSCOPE
  • Application of an existing probe set or custom probe set design (up to 500 genes targeted). Pricing is affected by the number of probes with currently 3 tiers supported: up to 140 targets, up to 300 targets, and up to 500 targets.
  • Consultation to identify optimal targets for a custom probe set using single cell and spatial data for the tissue/pathology of interest.
  • Full service including tissue pre-processing, probe design (optional), capture, scanning, and data analysis (optional)
  • Downstream data analyses are also supported (optional)
Vizgen MERSCOPE
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The Spatial Technologies Unit
The Spatial Technologies Unit provides access, training, education, and expertise on spatial or single cell technologies. It is open to all researchers from academia and industry.
Contact Info

330 Brookline Ave.
Dana Building
Beth Israel Deaconess Medical Center
Boston, 02115 MA, USA
617-735-2611
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