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Single Cell Gene Expression

Compared to bulk transcriptome sequencing, single-cell sequencing reveals the full complexity of cellular diversity. It addresses challenges associated with studying rare cell types, cell lineage relationships, and heterogeneous samples, facilitating the analysis of individual cell functions. Through in-depth single-cell analysis, researchers can efficiently discover new targets and biomarkers, advancing scientific discoveries.

Novogene offers comprehensive end-to-end single-cell sequencing services, including Single Cell 3′ Gene Expression, Single Cell 5′ Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC, etc. Our services provide comprehensive support for your projects, from experimental design consultation, onsite services*, library preparation, Next Generation Sequencing, and bioinformatics analysis reports.

As a Certified Service Provider of 10x Genomics and Illumina NGS platforms, you can trust the highest quality and reliability in our single-cell sequencing workflows.

*On-site single cell capture service is available to customers in Singapore and Japan only.


  • Single Cell Gene Expression: Profiling of cellular heterogeneity, novel targets, and biomarker in each cell from a heterogeneous cell population.
  • Single Cell Immune Profiling: Analyze full-length, paired B-cell or T-cell receptors, antigen specificity, and gene expression, all from a single cell.
  • Single Cell ATAC: Analyze chromatin accessibility at the single-cell level, providing insights into cell types and states, and deeper understanding of gene regulatory mechanisms*

*Do not provide single cell ATAC multiome service.

Sample Requirements

Sample Type Service Sample Amount Cell Viability
Fresh single cell suspension
Single nuclei suspension*
On-site service* Single Cells ≥ 1,000,000 Viability ≥ 80%, Diameter: 5-30 μm
Frozen single cell suspension** Shipping with dry ice Single Cells ≥ 1,000,000 Viability ≥ 80%, Diameter: 5-30 μm

* On-site service applies to Singapore and Japan customer only. Single nuclei suspension is available for on-site service only.

** Please download and complete the form if you are sending frozen single cells to us.

Specifications: Sequencing & Analysis

Sequencing Platform NovaSeq 6000 or NovaSeq X Plus
Read length Pair-end 150bp
Recommended Data 20,000 – 50,000 read pairs/cell, around 120Gb/sample
Analysis  Cell Ranger Analysis Standard Analysis
  • Demultiplex BCL files from a sequencer into FASTQs.
  • Summary metrics (sequencing quality, number of cells detected, the mean reads per cell, and the median genes detected per cell et al.).
  • Alignment of reads to genome.
  • Gene expression quantification.
  • Clustering analysis.
  • Differentially expression analysis between clusters.
  • Visualization.
  • Demultiplex BCL files from a sequencer into FASTQs.
  • Alignment, UMI counting, Metrics summary.
  • Identification of highly variable gene (HVGs).
  • Cell Subpopulation Identification.
    Principal component analysis (PCA).
    Identify clusters of cells.
    Dimensionality reduction and Visualization.
  • Marker gene detection (Differentially expression analysis between clusters).
  • GO/KEGG/Reactome Enrichment.
    FunctionalAnnotation of Transcription Factor.
    Protein-Protein Interaction Network Analysis.

Project Workflow

We support an end-to-end suite of services to ensure that our clients gets the best quality data – This includes a pre-project consultation with our application experts in experimental design, subsequent sample preparation, library construction, sequencing, data quality assurance, and bioinformatics analysis.

Our standard analysis package encompasses the identification of distinct cell populations and differential gene expression, equipping researchers with in-depth insights to drive their scientific discoveries forward. Leveraging the Cell Ranger analysis pipeline, we expertly manage raw sequencing data through meticulous quality control, precise alignment, and accurate quantification processes, transforming complex data into actionable insights.

Our experience spans an impressive array of over 300 species and sample types, encompassing a broad spectrum of biological systems from well-established model organisms to the rare and unique, such as the Siberian Tiger, Turtles, and Lungfish. This extensive experience ensures that we deliver robust and reliable results.

Featured customer publications

Demo Results

Figure 1 The t-SNE and UMAP plots

Note:Each point represents a cell, and each color designates a cluster.

For visualization purposes, dimensionality was further reduced to 2D using t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP). Both of them try to find a low-dimensional representation that preserves relationships between neighbors in high-dimensional space. Compared to t-SNE, the UMAP visualization tends to have more compact visual clusters with more empty spaces between them.

Figure 2 Expression Pattern of Marker Genes

Note: Darker red represents a higher expression level, and darker blue dictates a lower expression level.

Heatmaps show the expression of indicated marker genes for given cells and features. In this case, we plotted the top 10 markers (or all markers if less than 10) for each cluster.

Figure 3 Expression Level of Marker Genes

Note: The X-axis represents the cluster, and the Y-axis represents the expression level.

Violin plots show the relative expression levels of marker genes among all clusters. (Only six marker genes are shown here)