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Three Dimension Genomics, Inc.

5 Orders Completed
Carlsbad, California, US

About Three Dimension Genomics, Inc.

Three Dimension Genomics, Inc. is enabling next-generation drug development screens using High Throughput Screening, cell-based High Content Assays, cerebral organoids, and single-cell transcriptomics. We use our proprietary in vitro genetics platform in collaboration with Pharma partners to identify novel drug targets and elucidate molecular mechanisms of action. We also collaborate with government partners to determine pathways of toxicity for thousands of environmental toxicants. The power of our technologies will provide you a competitive advantage over those using traditional cell culture methods, biochemical assays, and bulk RNA-sequencing by saving you time and money.

Our Services (26)


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High Content Screening

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High content imaging assays will provide you with phenotypic data to select the best drug candidates early on in development and reduce the risks of costly failures later.  

Cell-based high content assays enable direct correlations between genetic alterations, disease phenotypes, and treatment effects.  If you want to access new mechanisms of action, look beyond traditional cytotoxicity assays and cancer cell lines. More disease-relevant models and multiplex phenotypic assays are needed to discover and confirm casual relationships between novel targets, MOAs, and phenotypic effects in order to expand into new arenas of therapies.

While cancer remains by far the most common therapeutic area where high content assays are utilized, they are highly applicable to other fields, especially to rare and orphan diseases where MOAs may be less characterized. 

We work with you to develop the most relevant multiplexed assay that will allow you to: 

  • evaluate several biomarkers or parameters in a single experiment;
  • thoroughly characterize a variety of cytotoxic effects in 2D or 3D human or animal primary and stem-cell derived cellular models;
  • assess not just levels of proteins, but also their cellular localizations and translocations from one organelle to another;
  • characterize structural and morphological changes; 
  • assess effects on rare cell populations.


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Cytotoxicity Assays

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Cell viability, proliferation, cytotoxicity and apoptosis

3D Genomics offers cytotoxicity evaluations that range from simple cell count to assays that provide a detailed view into the specific mechanisms of cell death and allow you to detect early cytotoxic effects that may not yet result in the reduction of cell number, such as changes in nuclear or mitochondrial morphology, expression of early apoptotic markers, changes in membrane permeability, etc. Testing can be performed in relevant cell models, including primary human hepatocytes, neuronal cells, co-cultures, 3D spheroids, and microtissues.  Additionally, a neurite outgrowth assay is available to specifically assess the health of neuronal cells in culture.

High content imaging High Content Analysis

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Organoids

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We specialize in the development of organoid models from ESC, iPSC and lineage restricted stem cells. Analysis methods focus on single cell technologies such as scRNAseq, high content imaging, and FACS analysis and sorting. We work with you to design the most appropriate experiment to fit your needs. Most of our studies have been with human and mouse cerebral organoids and we are adding other tissue organoid models. 

- Develop or establish organoid models from stem cell lines.  

- Conduct analysis of organoids across genetics, compound treatment, developmental stage, or combinations of the above. 

- Dissociate organoids and analyze at the single cell level.

- Identify cell types, determine transcriptomes, phenotypic and functional measures.

- Identify upregulated and downregulated genes/pathways to elucidate mechanism of action. 

 

Mouse Human CNS/Neurology Pain Psychiatry/Mental Health Alzheimers Disease Toxicology Drug Discovery Show 8 more tags Show less

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Single Cell RNA-Seq

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We conduct single cell RNAseq and bulk RNAseq experiments from samples that you provide. We can also establish conventional cell based models with human or nonhuman mammalian cell lines and conduct RNAseq as readout. Other plate based readouts can be added as desired (e.g., alphaLISA assays, RTCA label free assays, immunohistology assays from single well/slide to high content imaging, MEA assays etc).

10x Genomics Chromium System

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Transcriptomics Data Analysis

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We offer tailored bioinformatic analysis of your single cell or bulk transcriptomic data, which includes:

-Fastq demultiplexing, read alignments, UMI counting, data normalization, dimensionality reduction and clustering, pseudotime analysis, data visualization, identification of affected cell types, identification of up-regulated and down-regulated genes and pathways, and identification of master regulators and causal networks.


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Stem Cell Differentiation

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3D Cell Culture Models

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Toxicology

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Biology

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Computational Modeling

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Biostatistics & Bioinformatics

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Cells and Tissues

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Project Management

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RNA Sequencing

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Nucleic Acid Services

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Biochemistry & Molecular Biology

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Data Services

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RNA Services

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Pharmacology & Toxicology

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Drug Discovery

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Drug Discovery & Development

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Cell and Tissue Culture

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Mammalian Cell Culture

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Cell Line Authentication

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Induced Pluripotent Stem Cell (iPSC) Culture

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Genotyping and Gene Expression Assays

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Ted Choi

President and Chief Scientific Officer

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