Overview
Modern multiomics research demands the ability to profile gene expression, chromatin accessibility, protein abundance, and spatial tissue architecture, often on the same samples, and at single-cell or subcellular resolution.
Our core facility offers a fully integrated suite of single-cell and spatial multiomics technologies under one roof, enabling investigators to design cohesive, multi-platform workflows without fragmenting their projects. Whether your study calls for discovery-driven transcriptomics, high-plex spatial profiling, or a combination of both, we can support the full arc from sample to data analysis.
Single-Cell and Single-Nuclei Genomics
Our single-cell services are built around the 10x Genomics Chromium platform, the industry standard for high-throughput droplet-based library preparation, complemented by the QuantumScale platform for experiments requiring very large cell or nuclei numbers.
Available assays include:
- Single-cell/single-nuclei 3' or 5' RNA-seq: transcriptome-wide gene expression profiling at single-cell resolution
- Single-nuclei ATAC-seq: cell-level profiling of chromatin accessibility and open chromatin regions
- Multiome (RNA + ATAC): simultaneous transcriptomic and epigenomic profiling from the same nuclei
- Supported add-on options: V(D)J sequencing for immune repertoire analysis, CITE-seq for surface protein quantification, and cell or nuclei hashing for multiplexed sample processing
- Single-cell combinatorial indexing (Sci-seq) via the QuantumScale platform (formerly ScaleBio), a plate-based, instrument-free combinatorial barcoding approach well-suited for very large cell or nuclei numbers
- snPatho-seq (single-nucleus RNA-seq from FFPE): enables transcriptomic profiling at single-nucleus resolution from formalin-fixed, paraffin-embedded (FFPE) tissue blocks and archival slides, including legacy biobank material. This workflow extends the power of single-cell genomics to tissue repositories that would otherwise be inaccessible to dissociation-based approaches, opening the door to retrospective studies on clinically annotated cohorts.
Spatial Multiomics
Our spatial platforms allow gene expression and protein signals to be mapped directly within intact tissue sections, preserving the architectural context that dissociation-based approaches cannot capture. Critically, spatial and single-cell datasets generated in our facility are designed to be integrated: single-cell data can inform cell type deconvolution of spatial data, and spatial data can provide the tissue context to anchor single-cell findings. Importantly, both our snPatho-seq and Xenium workflows support FFPE tissue, meaning that retrospective and biobank-based studies can be pursued across multiple platforms in an integrated fashion.
Available platforms and workflows include:
- Xenium In Situ Analyzer (10x Genomics): high-sensitivity, subcellular-resolution in situ RNA profiling using custom or pre-designed gene panels, enabling highly multiplexed transcript detection with single-molecule precision.
- Xenium Multimodal (RNA + Protein): simultaneous in situ detection of RNA targets and protein markers within the same tissue section via antibody-based co-detection. Enables direct correlation of transcript and protein signals at subcellular resolution without serial sectioning or loss of spatial registration. Particularly powerful for cell type and state phenotyping in complex tissues.
- Integrated same-slide workflows: Our Xenium platform supports select pre- and post-run co-application workflows on the same tissue section, including multiplexed immunofluorescence (multi-IF), H&E staining, Visium HD, and MALDI mass spectrometry imaging.
- Visium HD (10x Genomics): whole-transcriptome spatial gene expression at near-cellular resolution using a high-density capture array. Suitable for FFPE or fresh-frozen tissue sections with no prior knowledge of target genes required.
Quality Control
All projects include RNA and DNA library quality assessment using our TapeStation 4200, which enables rapid, automated electrophoresis of up to 96 samples and provides RNA Integrity Numbers (RIN), DNA Integrity Numbers (DIN) and DV200 analysis for FFPE RNA samples.
Getting Started
Consultation on experimental design and workflow is required prior to beginning a project. Detailed pricing will be provided at that time. To schedule a consultation, or for any other questions, please email Dr. Barbara Rosati at barbara.rosati.1@stonybrook.edu.
Additional Support
- Assistance with sample preparation and tissue section optimization
- Troubleshooting support
- Flexible scheduling to accommodate clinical or animal sample processing timelines and schedules
- Bioinformatics support and data integration across modalities
- Assistance with grant applications (methods sections and letters of support)
Access
We currently serve internal investigators at Stony Brook University and Northport VAMC, and their collaborators. External service may be possible depending on the project, please contact Dr. Rosati for details.
Single Cell and Spatial Multiomics, Director: Barbara Rosati, PhD
✉ barbara.rosati.1@stonybrook.edu | ☎ (631) 444-7350
Single Cell and Spatial Multiomics Bioinformatics, Lead Scientist: David McKinnon, PhD