Three Dimension Genomics (3DG) is a contract research company specializing in end to end single cell and spatial multiomics. Over the last four years we have conducted dozens of single cell projects on the 10XGenomics Chromium platform across hundreds of cell samples. We specialize in spatial transcritpomics using the 10X Visium platform using frozen tissue samples, and we are excited to offer FFPE Visium, enabling spatial transcriptomic studies using your existing FFPE tissue and tumor samples.
We focus on single cell technologies including scRNAseq, high content analysis (HCA), FACS analysis and sorting. We are an end-to-end service partner, from designing the study with you to receiving cell or tissue samples, producing highest quality data through delivery of transcriptomes, images, gene expression tables, clustering and integration of multiomic datatypes toward a deeper understanding of your sample biology.
We have worked with multiple biotech companies and global pharma companies. Our projects range from pilot studies of <10 samples to multiomics studies on 100+ samples involving both spatial and single nuclei transcriptomics.
We specialize in single cell and spatial transcriptomic services using the 10XGenomics Chromium and Visium platforms. Frozen tissue and FFPE tissue samples can be used for Visium spatial transcriptomics. We can isolate nuclei from serial sections for single nuclei RNAseq in conjunction with Visium spatial studies, and can image markers of interest by fluorescent immunohistochem studies.
Spatial transcriptomics of FFPE tumor samples on the 10X Genomics Visium platform. In conjunction with spatial profiling we can isolate nuclei from serial sections for single nuclei RNAseq, and can image markers of interest by fluorescent immunohistochem.
TCR repertoire and clonotype analysis using 10X Genomics Single Cell Immune Profiling. Antigen specific T cells can be isolated from PBMCs by FACS using dextramers. Single cell RNAseq will be conducted on selected T-cells using the 10X Single Cell Immune Profiling platform. TCR VDJ regions will be sequenced. Optionally, 5’-end transcriptome scRNAseq can be conducted along with TCR VDJ sequencing.
Single Cell Multiomics on the 10X single cell platform. scATACseq + scRNAseq from the same cell, or scRNAseq + Protein panel by immunofeature tagging in the same cell.
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).
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.
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:
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.
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.
Three Dimension Genomics, Inc. has not received any reviews.
Three Dimension Genomics, Inc. has not received any endorsements.