Contact Info:

Spatial Technologies Unit

330 Brookline Avenue

ES-0B01A

Boston, MA 02115

https://www.spatialtechnology.org

Grants and Identifiers:

RRID: RRID:SCR_024905

Instrumentation:

Services Provided:

10x Genomics

10x Genomics Visium

10x Genomics Xenium

Akoya PhenoCycler Fusion

Brightfield Microscopy

Cell Imaging

CITE-seq

CODEX

Computational - Bioinformatics

Computational - High Performance Computing

Confocal/ Super Resolution Microscope

Consultations

Cryostat Histology

Customized Protocols

Data Analysis

Data Analysis And Interpretation

High-plex Immunofluorescence

Image Processing And Analysis

Immunofluorescence

Immunohistochemistry

In Situ Hybridization

Multiplex Fluorescence

Multiplexed Immunofluorescence

NanoString GeoMx DSP

Protocol Development

R Shiny App Development

Scanning 20X Brightfield

Scanning 20X Fluorescent

Scanning 40X Brightfield

Scanning 40X Fluorescent

Single Nucleus Dissociation & Sequencing (FFPE Or Frozen)

Single-cell Sequencing

Spatial / Single Cell Data Analysis

Spatial / Single Cell Training

Spatial Transcriptomics

Super-resolution Microscopy

Tissue Processing

Vizgen MERSCOPE

Relevant Publications:

1.) Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CG, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Gregory M, He S, Patrick M, Rane T, Wardhani A, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, (2025 Mar 14). A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients Genome Biology, 26(), 56. . PMCID: 11907808.

2.) Castanho I, Yeganeh PN, Boix CA, Morgan SL, Mathys H, Prokopenko D, White B, Soto LM, Pegoraro G, Shah S, Ploumakis A, Kalavros N, Bennett DA, Lange C, Kim DY, Bertram L, Tsai LH, Kellis M, Tanzi RE, Hide W (2025 Jan 15). Molecular hallmarks of excitatory and inhibitory neuronal resilience and resistance to Alzheimer’s disease bioRxiv, (), 2025.01.13.632801. . PMCID: 11761133.

3.) Wang S, Jiménez-Gracia L, De Amaral AA, Vlachos IS, Plummer J, Heyn H, Martelotto LG (2024 Sep 5). FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays Bio-protocol, 14(17), e5063. . PMCID: 11417608.

4.) Izumi M, Fujii M, Kobayashi IS, Ho V, Kashima Y, Udagawa H, Costa DB, Kobayashi SS (2024 Aug 9). Integrative single-cell RNA-seq and spatial transcriptomics analyses reveal diverse apoptosis-related gene expression profiles in EGFR-mutated lung cancer Cell Death & Disease, 15(8), 580. . PMCID: 11316060.

5.) Pilcher WC, Yao L, Gonzalez-Kozlova E, Pita-Juarez Y, Karagkouni D, Acharya CR, Michaud ME, Hamilton M, Nanda S, Song Y, Sato K, Wang JT, Satpathy S, Ma Y, Schulman J, D'Souza D, Jayasinghe RG, Cheloni G, Bakhtiari M, Pabustan N, Nie K, Foltz JA, Saldarriaga I, Alaaeldin R, Lepisto E, Chen R, Fiala MA, Thomas BE, Cook A, Dos Santos JV, Chiang IL, Figueiredo I, Fortier J, Slade M, Oh ST, Rettig MP, Anderson E, Li Y, Dasari S, Strausbauch MA, Simon VA, Rahman AH, Chen Z, Lagana A, DiPersio JF, Ros (2024 May 17). A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma bioRxiv, (), 2024.05.15.593193. . PMCID: 11118283.

Description:

The STU has been established to render cutting-edge spatial and single cell technologies accessible to all, as well as to provide expertise, training, and education to Academia and industry. By colocalizing spatial technologies with extensive supportive equipment (NGS, tissue processing, imaging, bioinformatics) the STU can provide specialized or A-to-Z spatial and single cell services, enabling researchers to focus on science and discovery. The STU can support diverse projects, starting from consultation, where we match the right technologies to the project’s needs, budget, and timeline. We perform all aspects of the single cell and spatial assays in house, including tissue preparations, staining, and sequencing, enabling us to control the timeline and quality of service. Finally, the STU can also support all downstream bioinformatic analyses for the generated single cell and spatial data. Services 10x Genomics Visium (v1 and v2 on the 10x Genomics CytAssist) A-to-Z hands off full service, from tissue (frozen, FFPE or already sectioned FFPE tissue ) to data on the 10x Visium Platform from 1 ( multiples of 4 is more cost-effective) to 100+ samples.Users can provide tissues (embedded or not), or even tissue already placed on Visium slides. We are also pioneering the use of already fixed slides through the use of the CytAssist by 10x Genomics.Visium services include: Optimized tissue pre-processing (FFPE or Frozen) for Visium Tissue staining compatible with Visium (H&E or Fluorescence) Visium slide and library prep Next Gen Sequencing & Data generation Space Ranger output and/or R Object preparation (optional) Downstream analysis (optional) 10x Genomics Xenium The 10x Genomics Xenium provides single cell and up to sub-cellular resolution, with the ability to tag and assign independent RNA molecules to quantify gene expression.The current services include: Tissue preparation (FFPE & frozen) and testing for use in the Xenium Application of an existing probe set or custom probe set design (up to 480 genes targeted) 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) Single Cell/Nucleus Sequencing (from Fresh, Frozen, and FFPE samples) The STU provides fully automated single cell and nucleus sequencing services, including immunoprofiling (VDJ sequencing). Automation minimizes variability and maximizes repeatability of findings. Single Cell/Nucleus services include: Single Cell Sequencing (3′ and 5′) on the 10x Genomics Connect Single Cell Immunoprofiling (expression and TCR/BCR sequencing) Single Nucleus Sequencing Fully automated single cell and nucleus suspension from tissue samples using the S2 Singulator Full service from tissue or cell/nucleus suspension to data, comprising dissociation (if required), encapsulation, library preparation, sequencing, and Cell Ranger/data analysis (optional) Ability to process Fixed and FFPE samples and difficult tissues. FFPE single nucleus sequencing is performed using the 10x Genomics X Chromium Controller and the snPATHOSeq protocol. Akoya PhenoImager HT (up to 8-plex Multiplexed Immunofluorescence, Whole Slide scanning) The PhenoImager HT whole slide scanner supports up to 7 fluorescent wavelengths (6 antibodies + DAPI) across the whole slide using MOTiF technology, in addition to standard brightfield imaging. It supports 20x (single cell) and 40x (sub-cellular) resolution, with extreme speeds (multiple slides per hour), enabling the investigation from one sample to large scale cohorts.Its high plexity mode supports up to 8 antibodies + DAPI.PhenoImager HT Services include: Automated staining on the Leica Bond Rx to minimize variability using an existing antibody panel. Design and generation of a custom panel + staining on the Leica Bond Rx + scanning on the Polaris. Scanning of already stained slides using fluorescence Analysis using the Akoya InForm software, enabling minimization of autofluorescence and optimal channel demultiplexing. Downstream analyses (optional) Akoya Phenocycler Fusion The Phenocycler Fusion enables high content imaging with the ability to multiplex dozens of antibodies (up to 65 in its current iteration) on a tissue section (FFPE or frozen), covering a large portion of a standard histology slide.Phenocycler Fusion Services include: Consultation on the selection of markers using single cell and spatial data. Design and generation of a custom panel + staining + data generation on the CODEX. Scanning of an already stained slide with CODEX-compatible panel. Analysis using the Akoya CODEX software Downstream data analysis (optional) Bruker Vutara VXL The Vutara VXL is extremely versatile enabling from tissue and live cell 3D imaging, to chromatin conformation and spatial investigations.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). Nanostring GeoMX DSP The NanoString GeoMx DSP enables spatial transcriptomics and proteomics on FFPE or frozen tissue sections.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 including the WTA (18,000+ genes quantified per region, the CTA 1,000+ genes quantified per ROI, and 570-plex antibody proteomics assays). Up to 90 ROIs per slide Full service (pre-processing, staining, ROI selection, data generation, data processing (optional) Downstream investigations (optional) Vizgen MERSCOPE The Vizgen MERSCOPE provides sub-cellular resolution, with the ability to tag and assign independent RNA molecules and quantify gene expression. The error correction algorithm and multiple probes assure high confidence in results. The resolution is optimal for rare cell type investigations, neuronal tissue studies, and complex heterogeneous tissues, such as tumors.The current services include: Tissue preparation (frozen) 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) Tissue Microarray Generation For all spatial investigations the number of slides is a factor affecting significantly cost and labor. The STU provides tissue microarray generation on the Epredia TMA Grandmaster, a fully automated high capacity system, supporting the creation of blocks with multiple donors and multiple regions of interest per donor.Services include: Tissue pre-processing (if not processed) TMA generation for small, medium, and large scale studies. Punch biopsy extraction of selected regions for additional preparations (e.g. Whole Exome Sequencing, RNA-Seq, etc). Training and Education The STU was established with a mandate to provide education and training on spatial and single cell technologies.The services include: Seminars, lectures, or talks on single cell/spatial technologies, as well as their application on specific domains. Hands on training of researchers and small groups on an instrument Workshops for specific technologies and/or data analysis Seminar series that can take place in our facilities, the client's, or remotely. High-level, strategy, IP, grant-writing, and leadership in light of the spatial technology revolution. Can be customized for physicians, PIs, investors, and leadership. Major Equipment: 10x Genomics Xenium: Latest generation transcriptomics instrument using fluorescence in situ hybridization. Up to 480 targets and the ability to perform orthogonal modalities on the same slide. 10x Genomics CytAssist: An imaging / tissue prep instrument, enabling the use of the new generation (v2) of 10x Genomics Visium reagents and the application of the Visium protocol on standard pathology slides (FFPE & Fresh Frozen). 10x Genomics Connect: The first completely automated robotics system for single cell library preparations, minimizing technical noise and batch-to-batch variation. It also maximizes throughput for large-scale single cell assays. 10x Genomics Chromium X: The new generation of the 10x Genomics Chromium Controller enabling us to go up to 1M cells per run or to perform single cell/single nucleus sequencing from FFPE samples. Akoya Polaris Vectra / PhenoImager HT: Next generation whole slide multispectral scanner with the ability to multiplex 8 antibodies (IHC) with minimal (or no) autofluorescence. Akoya CODEX: Highly multiplexed spatially resolved immunofluorescence assay, enabling the characterization of more than 50 protein markers in situ, at single cell resolution. Akoya PhenoCycler Fusion: Highly multiplexed spatially resolved immunofluorescence assay, enabling the characterization of more than 100 protein markers in situ, at single cell resolution. Bruker Vutara VXL: Super resolution microscope (below the diffraction of light limit nm resolution), with the ability to perform spatial studies, 3D reconstructions and real-time video capture of in vitro samples, organoids, and tissue. NanoString GeoMx DSP: Spatial transcriptomics / proteomics unit, with the ability to perform region-of-interest-based analyses with up to whole transcriptome (~18,000 genes or 570 antibodies) capture in situ. Vizgen MERSCOPE: Spatial transcriptomics technology enabling the streamlined acquisition of gene expression at high resolution (sub-cellular) for hundreds of targeted transcripts. It can be especially tailored for CNS/Neuron evaluations to capture RNAs across neurons. Leica Bond Rx: Automated unit for immunohistochemistry and in situ hybridization. 3DHISTECH TMA GrandMaster: Fully automated large scale tissue microarrayer with the ability to combine up to 558 (0.6 mm), 286 (1 mm), 135 (1.5 mm), 84 (2 mm) regions from up to 60 donors and up to 12 recipient blocks. The GTMA enables us to combine multiple FFPE samples for the optimal performance of spatial investigations. S2 Singulator: Automated tissue dissociator with the ability to generate cell suspensions or nucleus suspensions from tissue sections without manual intervention. Agilent Fragment Analyzer: State of the art instrument for quality assessment of NGS libraries as well as for the evaluation of RNA/DNA sample quality and properties. Nikon T2i Eclipse: Inverted microscope with a 25mm field of view (FOV) and large-format CMOS cameras, with the ability to capture brightfield (monochrome, color), and fluorescence. The scope is connected to a dedicated analysis server equipped with the Nikon Elements Software, with additional high-end packages enabling automated programmed captures, and large image stitching. Supporting equipment: Leica cryostat and microtome, laboratory refrigerators, -20 and -80 freezers, thermocyclers, etc. Instrument Workstations: the Vutara, Akoya CODEX and Polaris, and the Nikon Eclipse are all connected to independent (at least one per instrument) dedicated analysis server and/or workstations with Xeon processors and high RAM capacity. A local NAS (~100TB) is used to capture data generation. Nikon Elements, Akoya CODEX Processor and InForm Tissue Analysis Software are installed to the systems.