Single Cell Long Read Transcriptome

Long-read single-cell transcriptome profiling to resolve full-length isoforms and reveal transcriptional complexity at single-cell resolution.

Single-cell sequencing has traditionally relied on short-read sequencing, which effectively provides insights into single-cell gene expression, but falls short in capturing information about alternative splicing, splicing regulation, transcriptomic complexity, and isoform diversity.

The incorporation of long-read sequencing into single-cell assays addresses this shortfall observed in traditional short-read sequencing methodologies. This integration offers insights into molecular mechanisms, enabling the identification of intricate structural variants, comprehensive exploration of whole transcript alternative splicing events, and the expression of cell-type-specific mRNA isoforms at the single-cell level.

Why Choose Novogene for Single Cell Long Read Transcriptome Sequencing?

Proven Expertise

Delivered 200+ single-cell long-read RNA-seq projects with fast turnaround and reliable results

Enhanced Sample Processing

Flexible workflows including nuclei extraction and optimized pipelines for frozen tissue samples

Advanced Technology & Certified Excellence

10x Chromium X with GEM-X, plus Illumina and Nanopore for short- and long-read sequencing

Cost-Effective Solutions

Cost-effective long-read single-cell solutions with high-throughput platforms, expert support, and high-quality data

Fast Turnaround

High‑quality sequencing data delivered in as little as two weeks to keep your project moving forward efficiently.

Multi‑Omics Integration Capability

Seamless integration with WES, transcriptome, and epigenome platforms provides deeper biological and functional insights.

Applications of Single Cell Long Read Transcriptome Sequencing

Unlock comprehensive insights into human genetics for hereditary disease, cancer, and population studies.

Single-cell Level Isoform Discovery & Quantification

Unambiguously identifies and quantifies full-length splice variants. This is crucial for understanding functional diversity in complex tissues like the brain or cancer.

Single-cell Level Fusion Gene Detection

Long reads span entire fusion breakpoints, enabling precise detection of complex oncogenic gene fusions in single cancer cells.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

We support an end-to-end suite of services to ensure that our clients get 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.

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Demo Results

1/3

UMAP Plots Showing Cell Clusters and Cell Types

1/3

S100A4 Gene Expression and S100A4 Isoform Distribution

The expression level of the S100A4 gene does not show cell‑type specificity, but its isoforms exhibit differential expression across distinct cell populations.

1/2

Fushion Gene Detection

SDC4:SH3PXD2B fushion gene can only be identified through Long-read sequencing result.

More Services

Single Cell Gene Expression

Single Cell Immune Profiling Sequencing

Visium HD Spatial Gene Expression

Ready to Start Your Project?

Our platform offers tailored solutions for

your unique experimental needs, ensuring a seamless experience from project design to data delivery.

Single Cell Long Read Transcriptome

Long-read single-cell transcriptome profiling to resolve full-length isoforms and reveal transcriptional complexity at single-cell resolution.

Why Choose Novogene for Single Cell Long Read Transcriptome Sequencing?

Proven Expertise

Delivered 200+ single-cell long-read RNA-seq projects with fast turnaround and reliable results

Enhanced Sample Processing

Flexible workflows including nuclei extraction and optimized pipelines for frozen tissue samples

Advanced Technology & Certified Excellence

10x Chromium X with GEM-X, plus Illumina and Nanopore for short- and long-read sequencing

Cost-Effective Solutions

Cost-effective long-read single-cell solutions with high-throughput platforms, expert support, and high-quality data

Fast Turnaround

High‑quality sequencing data delivered in as little as two weeks to keep your project moving forward efficiently.

Multi‑Omics Integration Capability

Seamless integration with WES, transcriptome, and epigenome platforms provides deeper biological and functional insights.

Applications of Single Cell Long Read Transcriptome Sequencing

Unlock comprehensive insights into human genetics for hereditary disease, cancer, and population studies.

Single-cell Level Isoform Discovery & Quantification

Unambiguously identifies and quantifies full-length splice variants. This is crucial for understanding functional diversity in complex tissues like the brain or cancer.

Single-cell Level Fusion Gene Detection

Long reads span entire fusion breakpoints, enabling precise detection of complex oncogenic gene fusions in single cancer cells.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

Sample Type	Sample Amount
Single cell suspension	≥ 1,000,000 cells
cDNA from 10x Genomics	≥ 50 ng

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Sequencing Platform	Illumina NovaSeq System	Nanopore PromethION
Read length	Paired-end 150bp	Median read length: ~700-1000bp
Recommended Data Output	50,000 pair reads/cell 100-120Gb	1 PromethION Flow Cell ~100 M total reads/cell
Data QC Analysis	Cell Ranger 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	Wf-single-cell Data QC Identify the cell barcode and UMI sequences present in Nanopore sequencing reads Summary metrics (read quality, number of cells, genes and transcripts identified within each sample, median genes per cell, and sequence saturation) UMAP projections
Standard Analysis	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 Functional Annotation of Transcription Factor Protein-Protein Interaction Network Analysis	Data QC Mapping and Quantification Seurat analysis: Dimensionality reduction, clustering, and differential analysis Base on gene Base on transcripts (isoform) GO/KEGG/Reactome Enrichment Analysis Alternative Splicing Fushion Gene Detection

Project Workflow

Demo Results

1/3

UMAP Plots Showing Cell Clusters and Cell Types

1/3

S100A4 Gene Expression and S100A4 Isoform Distribution

The expression level of the S100A4 gene does not show cell‑type specificity, but its isoforms exhibit differential expression across distinct cell populations.

1/2

Fushion Gene Detection

SDC4:SH3PXD2B fushion gene can only be identified through Long-read sequencing result.

More Services

Single Cell Gene Expression

Single Cell Immune Profiling Sequencing

Visium HD Spatial Gene Expression

Ready to Start Your Project?

Our platform offers tailored solutions for

your unique experimental needs, ensuring a seamless experience from project design to data delivery.