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Single Cell Sequencing

Introduction to Single Cell Sequencing

Single Cell Sequencing reveals the full complexity of cellular diversity compared to bulk sequencing. It is primarily employed to solve complications related to the study of unusual cell types, cell-lineage associations, and samples of heterogeneous nature. By doing the in-depth single-cell sequencing, the cell functions of individual cells can be explored easily and efficiently.

By combining the 10x Genomics Chromium system and Illumina NGS platform, Novogene offers high-quality end-to-end single cell sequencing solutions and services, including Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC, etc. As a Certified Service Provider of 10x Genomics, Novogene provides efficient and accurate support for your research.

Applications of Single Cell Sequencing

  • 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 *

* : Only acceptable in AMEA (Asia pacific, Middle Eiddle East and Africa)

Benefits of Single Cell Sequencing

  • Single-cell sequencing intends to unveil the diversity of the transcriptome in heterogeneous cell samples. It provides deeper insights into 3’ and 5’ gene expression and characterizes cell differences, at a single-cell resolution.
  • Novogene provides an end-to-end package of single-cell sequencing solutions making use of the latest technology on the market: 10x Genomics Chromium system and Illumina NGS platform. We offer high throughput and high accuracy single-cell sequencing service, coupled with a fast turnaround time.

10x Single Cell Sequencing Specifications: Sample Requirements

Single cells suspension
Single nuclei suspension*
  • Fresh Tissue**
  • Frozen Tissue**
Service specifications for AMEA (AsiaPacific, Middle East and Africa) Service specifications for America

Note: 10x Single Cell sequencing service is only available in America and AMEA. Please refer to the service specifications of your region or contact your local sales.

10x Single Cell RNA Sequencing Specifications: Sequencing & Analysis

Sequencing Platform Illumina NovaSeq 6000 Sequencing System
Read length Paired-end 150bp
Recommended Data Amount ~150G raw data per sample
Content of Data Analysis
  • 10x sequencing data processing and quality control
  • Identification of highly variable genes (HVGs)
  • Cell subpopulation identification
  • Marker gene detection
  • Enrichment analysis and annotation of marker genes

Novogene Workflow of 10x Single Cell Sequencing Service

From sample preparation, library preparation, sequencing and data quality control, to bioinformatics analysis, Novogene provides high-quality products and professional services. Each step is performed in agreement with a high scientific standard and meticulous design to ensure high-quality research results. 

Featured publications of 10x Single Cell Sequencing

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)