SINGLE-CELL TRANSCRIPTOMICS

Single-Cell & Single-nuclei RNA-seq

Our boutique CRO has completed 100s of complex RNA sequencing projects over the years making us highly qualified to tackle the unique conditions of your science.

Why perform single-cell sequencing?

Single-cell RNA sequencing (scRNA-seq) provides a high-resolution view of gene expression at the individual cell level. It uncovers cellular diversity, identifies rare populations, and drives discoveries across fields like cancer, immunology, and neuroscience. With scRNA-seq, researchers gain insights that bulk methods simply can’t reveal.

Diagram contrasting single-cell and bulk gene expression analysis. Single-cell analysis examines individual cells, revealing cell-specific expression and heterogeneity. Bulk analysis averages expression from all cells, masking heterogeneity.

Single-cell or single-nuclei?

A magnified view of a biological cell with a translucent blue outer layer and a distinct orange nucleus, surrounded by other blurred cells on a blue background, representing cellular structure.

Single-cell RNA-seq (scRNA-seq)

Single-cell RNA-seq (scRNA-seq) uses intact, whole cells and captures the full cytoplasmic and nuclear transcriptome. It’s ideal when you can obtain high-quality, viable cells, such as from fresh tissues, blood, or cultured cells. You get a richer, more complete expression profile — but it requires careful handling to preserve cell integrity.

  • Use single cells when you want the fullest possible transcriptome and have access to fresh, viable samples.
A large, textured orange sphere in sharp focus, surrounded by several smaller, blurred orange spheres against a solid blue background, resembling particles or abstract cells.

Single-cell nuclei RNA-seq (scnRNA-seq)

Single-nucleus RNA-seq (snRNA-seq) isolates just the nuclei and profiles nuclear RNA. It’s often used when intact cells are hard to obtain — like from frozen, archived, or tough tissues (e.g., brain, fibrotic tissue). It also reduces biases from dissociation stress (which can alter cell states) and can be a better choice when dealing with fragile or complex samples.

  • Use single nuclei when working with frozen, delicate, or hard-to-dissociate tissues — or when minimizing stress artifacts is critical.

Our Process

Tissue Cells
01

What you provide

  • Tissue samples or single-cell suspensions

  • Single-cell suspensions should be at a minimum concentration of 400 cells/ul with a viability greater than 70%, with at least 50K cells total per sample.

What 3D Genomics provides

  • Cell preparation including dissociation, dead cell removal and/or nuclei isolation, if applicable, the Miltenyi GentleMACS Octo tissue dissociator is used for the purpose of improving the yield and quality of dissociated cells 
  • Single cell isolation, cDNA Synthesis and library preparation including QC for sequencing. 3D Genomics works with all 10x Genomics as well as other available single cell assays.
  • Sequencing, read mapping and alignment using CellRanger as well as other pipelines and informatic tools.
02
Library Preparation
Nuclei being analyzed on a monitor
03

What 3D Genomics delivers

  • Raw sequencing files (FASTQ) and sequencing QC report.
  • For 10x Assays the 10x CellRanger output: web summary, feature-barcode matrices, BAM files, automated secondary analyses, Loupe browser files and other output files
  • Computational support including clustering, cell type annotation and multiomic integration, if applicable
  • Remaining tissue samples will be discarded or returned, as per your instructions

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.

Gloved hands tending to multiple petri dishes containing green biological cultures or plant tissue on a white laboratory shelf.
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