Three Dimension Genomics, Inc.

About Us

Science Driven. Client Focused.

Three Dimension Genomics (3DG) is a boutique contract research organization based in Carlsbad, California specializing in single-cell transcriptomics, spatial transcriptomics, and skin biology. We work primarily with pharmaceutical and biotech companies that need more than a sample processing service. To our clients, we are a scientific partner embedded in their thinking from study design through final interpretation.

We don’t run generic pipelines. Every project gets custom experimental design, dedicated compute time on our in-house infrastructure, and analysis built around your biological questions. Our team holds PhD-level expertise in computational biology, genomics and experimental skin biology. 

Our clients include pharmaceutical companies, large and small biotech companies, and prestige global skincare and esthetics companies. Common engagements include mechanism-of-action studies, spatial profiling of clinical tissue, ex vivo skin models, and single cell studies of tissues and cell culture models. We’re also available through Scientist.com and Science Exchange for clients who need streamlined procurement.

Trusted by pharma, biotech, and academic research groups.

A scientist is using a pipette in a lab with test tubes and a computer showing DNA.
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Additional CRO Services

While single-cell and spatial transcriptomics are our core expertise,

we offer a broader range of assays and services to support our clients’ research programs.

Skin Biology

3DG offers ex vivo skin tissue studies with histological, immunofluorescence, and transcriptomic readouts. We also conduct in vitro studies on primary human dermal cells. Whether you’re evaluating an active ingredient or characterizing tissue response, we provide the biological system and the analytical expertise to answer your questions.

Contact Us about Skin Biology at 3DG
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High Resolution Imaging

  • Biomarker imaging for spatial multiomics
  • Proteomic vaildation of spatially distinct cell states
A diagram illustrating flow cytometry, showing different cell types (cytotoxic T-lymphocytes, T helper lymphocytes, other leukocytes) with specific surface markers (CD3, CD4, CD8) passing through a flow cell where they are illuminated by a laser and detected by a sensor. The resulting fluorescence data is presented as a 2-dimensional dot plot and 1-dimensional histograms, identifying 60% CD4-positive cells and 25% CD8-positive cells.

FACS isolation of Cell Subsets

  • Bulk cell enrichment by magnetic bead isolation
  • Antibody specific cell type isolation by FACS
JavaScript code being displayed on a monitor

In-Depth Bioinformatics

  • Detailed informatics and data visualization
  • Data integration for multiomics
  • Custom analysis workflows
Four fluorescent microscopy images comparing 'Cleared' (cyan, left) and 'Expanded' (magenta, right) cellular spheroids, with 'Endogenous' (top) and 'Immuno-stain' (bottom) fluorescent signals. Expanded spheroids are dramatically larger and reveal finely resolved internal cellular structures compared to the more compact cleared samples. White dashed lines indicate the approximate center of each spheroid.

High Content Imaging

  • High Content Analysis/Screening
  • 2D, co-culture, 3D imaging
  • Drug response HCS
  • Cell Painting assay
A diagram illustrating the transfer of 'required volumes' from four individual 96-well compound plates (green, blue, red, orange) into a single 384-well destination plate. Each 96-well plate fills one distinct quadrant of the 384-well plate. An inset shows how the A1 wells from each of the four 96-well plates contribute to specific sub-wells within the A1 area of the 384-well plate.

Custom Assay Development

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

Ready to move your spatial and single cell research forward?

Partner with 3D Genomics for high-resolution spatial and single-cell transcriptomics services that move your research forward.

Let’s Talk
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