Bioinformatics Support Unit

SpaRTAN

SpaRTAN

Spatially Resolved Transcriptomics

SPARTAN: Spatially Resolved Transcriptomics At Newcastle

Our Mission

Spatial Transcriptomics is a powerful technology which allows the whole transcriptome to analysed within a positional context; enabling sequencing data to be visualised directly on a tissue histology section.

Single cell resolution (up to 2µm) analysis can be achieved to uncover novel cell types and provide unique insights in to cell-cell interactions.

Expertise at every stage

SpaRTAN is a coalition of experts drawn from the University’s Human Developmental Biology Resource (HDBR), Bioimaging Facility, Genomics Core Facility, and Bioinformatics Support Unit.

Beginning with advice on experimental design and tissue preparation, the team provide a comprehensive service delivery startring with  tissue quality control verification, through the entire spatial transcriptomics process and the delivery of results in an easy to interpret and visualise form, ready for immediate interpretation. We can also make provide the material required for the analysis available via the various Newcastle Biobanks, including tumour and disease patient samples, as well as early human developmental tissue.

SpaRTAN are accredited have been Certified Service Provider of the Visium spatial transcriptomics platform with 10X Genomics since 2020.

10X Genomics Certified Service Provider for Visium Spatial Transcriptomics

Section of mouse brain with spatial transcriptomics data overlaid.

Available Services

SPATIAL TRANSCRIPTOMICS SERVICES

  • Single cell spatial analysis
    • Analyse the entire transcriptome from a whole tissue section.
    • *NEW* Up to 2µM resolution.
    • Compatible with frozen and FFPE tissues as well as material previously sectioned to microscope slides.
    • Combined histological and gene expression data.
    • Discover new biomarkers, identify novel cell types and states
  • Protein and RNA analysis on same section
    • Pre-defined antibody protein panels (30 proteins + controls) can provide protein expression in the same section as whole transcriptome analysis.
    • Fluorescent immuno-histochemistry enables key marker cells to be identified within the tissue section.
  • Bioinformatics data analysis
    • Standard analysis provides data in a format for immediate interpretation.
    • If required, further project specific analysis can be provided.
  • CytAssist instrument
    • Enables analysis to be performed on material sectioned to microscope slides.
    • Probe hybridisation is controlled to provide optimal target binding.
  • Single cell sequencing from FFPE tissue sections

Workflow

Applications

  • Analysis of healthy versus disease states including tumour and degenerative disease.
  • Spatial assessment of therapeutics on specific cells
  • Analysis of animal models
  • Human developmental studies

Benefits

Key benefits of Spatial Transcriptomics at NU:

  • Team of specialists at each step of the workflow
  • Extensive experience working with a broad range of tissues
  • Sample Flexible
  • Full tissue coverage
  • High Cellular Resolution
  • High Quality, Reproducible Results
  • In-depth Data Analysis

Sample Requirement

Tissues samples that are compatible with the established 10x Genomics Visium workflow:

  1. Fresh frozen tissue (embedded in OCT)
  2. Formalin-fixed paraffin-embedded (FFPE) tissue blocks
  3. Fixed frozen tissue
  4. FFPE/fresh frozen/fixed frozen section pre-cut on regular microscopic slides 
  5. Archived hematoxylin & eosin (H&E) stained FFPE slides

Sample RNA quality will be examined with Bioanalyzer after extraction by core staff. Only samples that pass the QC step will be accepted for spatial transcriptomic service.

Tissues samples that are compatible with the established workflow:

  1. Fresh frozen tissue (embedded in OCT)
  2. Formalin-fixed paraffin-embedded (FFPE) tissue blocks.

Service Request

FAQ

Technology

The service is enabled by the combination of four specialist services at Newcastle University:

Publication

1.            Queen R, Crosier M, Eley L, Kerwin J, Turner JE, Yu J, et al. Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves. PLoS Genet. 2023;19(11):e1010777.

1.            Walls GM, Ghita M, Queen R, Edgar KS, Gill EK, Kuburas R, et al. Spatial Gene Expression Changes in the Mouse Heart After Base-Targeted Irradiation. Int J Radiat Oncol Biol Phys. 2023;115(2):453-63.