understand your cells in context

Spatial transcriptomics, Single cell transcriptomics and multiomics on demand

Research Services at single cell resolution

We are a contract research company specializing in spatial transcriptomics and single cell transcriptomics. We also offer a full range of related single cell analytic technologies for complete, end to end project support.

Over the last four years we have conducted dozens of single cell projects on the 10X Genomics Chromium and Visium platforms for the biopharmaceutical industry.

We are an end-to-end service partner, from designing the study with you to delivering the highest quality transcriptome, proteome and quantitative image data.

We have worked with multiple biotech and pharma companies. Our projects range in scale from pilot studies of <10 samples to multiomics studies on 100+ samples.

Spatial Transcriptomics

We use the Visium spatial gene expression technology from 10X Genomics. We work with fresh frozen tissue or FFPE samples. We cut sections, produce H&E images and spatial libraries and sequence to the desired read depth. We map the reads to the target genome and conduct basic QC and cluster analysis using SpaceRanger, Loupe Browser and Seurat. All data are property of the client. All unused materials are returned to client. 

Spatial Transcriptomics
Spatial Transcriptomics

Single Nuclei and Single Cell Transcriptomics

We can obtain single nuclei gene expression data from serial sections of the tissue blocks used for spatial transcriptomics. Spatial and single nuclei gene expression are integrated using Seurat and similar tools.

We also provide standalone single cell gene expression services (without Visium). We work with frozen cells provided by the client, and also established custom cell culture models for client drug response studies and collected functional data, image data, and/or molecular data in addition to the single cell RNAseq data.

Related and Additional Services

Confocal Imaging

Confocal Imaging

  • Biomarker imaging for spatial multiomics
  • Proteomic vaildation of spatially distinct cell states
FACS isolation of Cell Subsets

FACS isolation of Cell Subsets

  • Bulk cell enrichment by magnetic bead isolation
  • Antibody specific cell type isolation by FACS
Single Cell Immune Profiling

Single Cell Immune Profiling

  • Comprehensive Immune Profiling
  • BCR/TCR profiling
  • Antigen specific TCR clonotype profiling with dCode dextramers
In-Depth Bioinformatics

In-Depth Bioinformatics

  • Detailed informatics and data visualization
  • Data integration for multiomics
  • Custom analysis workflows
High Content Imaging

High Content Imaging

  • High Content Analysis/Screening
  • 2D, co-culture, 3D imaging
  • Drug response HCS
  • Cell Painting assay
Custom Assay Development

Custom Assay Development

  • Compound validation assays
  • Complex dosing schemes
  • Full gamut of phenotypic and molecular readouts

What People Say

3DG has done an excellent job of experiment design, execution and data analysis

Professor UC Irvine & Chief Medical Officer,

Pharma Co

We were very pleased with the adaptability, responsiveness and quality of scientific thinking, data production and analysis

Early Stage Biotech Co

Pharma Co

Thank you so much for the feedback, explanations and insights you have given us

Research Director,

Global Pharma Co, UK

Based on our positive experience and the results of that first study, we conducted two more follow-on single cell RNAseq studies

Head of Research,

Large Biotech Co