Whole Transcriptome Sequencing

Comprehensive sequencing of the whole transcriptome to characterize coding and noncoding RNA expression, transcript structure, and regulatory complexity.

Whole Transcriptome Sequencing (WTS) is a comprehensive next generation sequencing (NGS) approach that profiles the full range of RNA molecules within a sample, including mRNA, long non coding RNAs (lncRNAs), and other non coding RNA species. By capturing both coding and regulatory transcripts, WTS provides an in depth and unbiased view of the entire transcriptome.

Novogene’s Whole Transcriptome Sequencing delivers a holistic analysis of transcriptional activity by enabling simultaneous identification, quantification, and characterization of diverse RNA species in a single assay. This workflow supports the exploration of complex RNA interactions, regulatory networks, and transcriptome wide expression patterns, offering powerful insights into how RNA molecules coordinate biological processes, influence disease development, and shape cellular function. Through this multi layered analysis, Novogene WTS enhances understanding of global gene expression regulation and the molecular mechanisms driving phenotypic outcomes.

Benefits of Whole Transcriptome Sequencing (WTS)

Comprehensive Transcript Detection

Simultaneously identify and quantify all major RNA types—including mRNA, lncRNA, circRNA, sRNA, and other non coding RNAs—providing a complete, high sensitivity view of the transcriptome.

Extensive Project Experience & Reliable Performance

Leverage Novogene’s deep expertise across large scale whole transcriptome sequencing projects to support robust investigations into gene expression regulation, biological pathways, and disease mechanisms.

Integrated Multi RNA Analysis & Functional Insight

Access end to end analysis covering transcript identification, expression profiling, differential expression, functional annotation, and regulatory network construction—all within a unified workflow that interprets interactions across multiple RNA species.

Multi Layered Regulatory Understanding

Gain insight into transcriptional and post transcriptional regulation, including interactions between coding and non coding RNAs, co expression relationships, and regulatory network architecture.

Publication Ready Bioinformatics Support

Receive expert curated, publication quality bioinformatics outputs—complete with visualizations, annotations, and summaries customized for high impact journal submission or downstream validation.

Benefits of Whole Transcriptome Sequencing (WTS)

Comprehensive Transcript Detection

Simultaneously identify and quantify all major RNA types—including mRNA, lncRNA, circRNA, sRNA, and other non coding RNAs—providing a complete, high sensitivity view of the transcriptome.

Extensive Project Experience & Reliable Performance

Integrated Multi RNA Analysis & Functional Insight

Multi Layered Regulatory Understanding

Gain insight into transcriptional and post transcriptional regulation, including interactions between coding and non coding RNAs, co expression relationships, and regulatory network architecture.

Publication Ready Bioinformatics Support

Receive expert curated, publication quality bioinformatics outputs—complete with visualizations, annotations, and summaries customized for high impact journal submission or downstream validation.

Applications of Whole Transcriptome Sequencing (WTS)

Whole Transcriptome Sequencing (WTS) enables a comprehensive examination of all RNA molecules within a biological system, supporting a wide range of research and translational applications.

Pan RNA Identification and Profiling

Discover novel transcripts and accurately quantify expression levels across mRNAs, lncRNAs, and other non coding RNAs. WTS enables characterization of transcript structure, isoforms, and functional attributes across the entire transcriptome.

Disease Mechanism and Biomarker Discovery

Analyze multi type RNA expression patterns in healthy and diseased states to identify diagnostic, prognostic, and predictive biomarkers. WTS supports the investigation of molecular pathways and mechanisms underlying cancer, metabolic disorders, neurological conditions, and other diseases.

Transcriptional & Post Transcriptional Regulation

Interrogate complex gene regulatory networks, including transcriptional control, alternative splicing, and non coding RNA mediated regulation. WTS reveals how regulatory RNAs influence gene expression, interact with coding transcripts, and coordinate cellular responses.

Therapeutic Target Discovery & Functional Studies

Characterize RNA molecules with potential as therapeutic targets and evaluate their functional roles in development, cell signaling, stress response, and disease progression. WTS provides a foundational dataset for mechanistic studies, pathway analysis, and drug target prioritization.

Applications of Whole Transcriptome Sequencing (WTS)

Whole Transcriptome Sequencing (WTS) enables a comprehensive examination of all RNA molecules within a biological system, supporting a wide range of research and translational applications.

Pan RNA Identification and Profiling

Disease Mechanism and Biomarker Discovery

Transcriptional & Post Transcriptional Regulation

Therapeutic Target Discovery & Functional Studies

Specifications

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Novogene’s Whole Transcriptome Sequencing (WTS) workflow begins with comprehensive sample quality control (Sample QC) to verify that RNA integrity and purity meet sequencing requirements. After QC, an appropriate library type—lncRNA/mRNA, circRNA, or small RNA—is prepared according to the project design and organism, followed by library quality control (Library QC) to confirm library performance.

Sequencing is then carried out using a paired‑end 150 bp (PE150) strategy for lncRNA and circRNA libraries, and a single‑end 50 bp (SE50) strategy for small RNA libraries. The resulting reads undergo rigorous data quality control (Data QC) before being processed through Novogene’s standardized bioinformatics pipeline.

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS workflow.

Novogene Whole Transcriptome Sequencing 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS workflow.

Specifications

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS workflow.

Resources

1/1

Differential Gene Expression Statistics

Summarizes the number of up‑regulated and down‑regulated genes across each comparison group, providing an overview of expression changes between conditions.

1/1

Interaction Analysis of Differential lncRNA Targets and mRNAs

Visualizes the relationships between differentially expressed lncRNA target genes and differentially expressed mRNAs. Categories include: up_mRNA, up_lncRNA_target, down_lncRNA_target, and down_mRNA.

1/1

circRNA–miRNA–mRNA Triplet Counts and Networks

Identifies and quantifies circRNA–miRNA–mRNA regulatory triplets in which all three components are differentially expressed, and constructs interaction networks for each comparison group.

1/1

GO Enrichment Analysis (Scatter Plot)

The scatter plot displays enriched GO terms, where the x‑axis represents the ratio of differentially expressed genes associated with each GO term, and the y‑axis lists the corresponding GO categories.

Frequently Asked Questions

What does Whole Transcriptome Sequencing (WTS) profile?

WTS captures all major RNA types, including mRNA, lncRNA, circRNA, miRNA, and other non coding RNAs, offering a complete and unbiased view of the transcriptome.

How is WTS different from mRNA seq or Total RNA seq?

What library types are used for WTS?

How much sequencing depth is recommended?

Can WTS identify novel RNA species?

What downstream analyses are included?

Does WTS support multi RNA regulatory network analysis?

Can WTS detect circRNAs?

What deliverables will I receive?

What sample types are accepted?

More Services

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Full-Length Transcriptome Sequencing

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Our platform offers tailored solutions for your unique experimental needs, ensuring a seamless experience from project design to data delivery.

Whole Transcriptome Sequencing

Comprehensive sequencing of the whole transcriptome to characterize coding and noncoding RNA expression, transcript structure, and regulatory complexity.

Benefits of Whole Transcriptome Sequencing (WTS)

Comprehensive Transcript Detection

Simultaneously identify and quantify all major RNA types—including mRNA, lncRNA, circRNA, sRNA, and other non coding RNAs—providing a complete, high sensitivity view of the transcriptome.

Extensive Project Experience & Reliable Performance

Integrated Multi RNA Analysis & Functional Insight

Multi Layered Regulatory Understanding

Gain insight into transcriptional and post transcriptional regulation, including interactions between coding and non coding RNAs, co expression relationships, and regulatory network architecture.

Publication Ready Bioinformatics Support

Receive expert curated, publication quality bioinformatics outputs—complete with visualizations, annotations, and summaries customized for high impact journal submission or downstream validation.

Benefits of Whole Transcriptome Sequencing (WTS)

Comprehensive Transcript Detection

Simultaneously identify and quantify all major RNA types—including mRNA, lncRNA, circRNA, sRNA, and other non coding RNAs—providing a complete, high sensitivity view of the transcriptome.

Extensive Project Experience & Reliable Performance

Integrated Multi RNA Analysis & Functional Insight

Multi Layered Regulatory Understanding

Gain insight into transcriptional and post transcriptional regulation, including interactions between coding and non coding RNAs, co expression relationships, and regulatory network architecture.

Publication Ready Bioinformatics Support

Receive expert curated, publication quality bioinformatics outputs—complete with visualizations, annotations, and summaries customized for high impact journal submission or downstream validation.

Applications of Whole Transcriptome Sequencing (WTS)

Whole Transcriptome Sequencing (WTS) enables a comprehensive examination of all RNA molecules within a biological system, supporting a wide range of research and translational applications.

Pan RNA Identification and Profiling

Disease Mechanism and Biomarker Discovery

Transcriptional & Post Transcriptional Regulation

Therapeutic Target Discovery & Functional Studies

Applications of Whole Transcriptome Sequencing (WTS)

Whole Transcriptome Sequencing (WTS) enables a comprehensive examination of all RNA molecules within a biological system, supporting a wide range of research and translational applications.

Pan RNA Identification and Profiling

Disease Mechanism and Biomarker Discovery

Transcriptional & Post Transcriptional Regulation

Therapeutic Target Discovery & Functional Studies

Specifications

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS workflow.

Specifications

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

Sample Requirements

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

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	Animal ≥ 7.5, Plant ≥ 7, with smooth baseline	A260/280 = 1.8-2.2; A260/230 ≥ 1.8;

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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS 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 X Plus Sequencing System
Read length	Paired-end 150bp for lncRNA/circRNA librarySingle-end 50bp for small RNA library
Recommended Data Amount	≥ 40 million read pairs per sample (lncRNA library); 10-20 million reads per sample (small RNA library);
Data Quality	Guaranteed ≥85% bases with Q30 or higher
Standard Analysis includes lncRNA, mRNA, miRNA, circRNA, and integrated association analyses.	• lncRNA: QC, mapping, AS, prediction, DE, SNP/InDel, lncRNA–mRNA interactions, GO/KEGG, PPI, fusion • miRNA: QC, length, mapping, annotation, novel miRNA, editing, family, expression • mRNA: QC, expression, DE, functional analysis, novel transcripts, SNP/InDel, AS, fusion, PPI • circRNA: QC, mapping, identification, expression, source‑gene mapping, DE, GO/KEGG, target prediction • mRNA–miRNA: Targeting, GO/KEGG, regulatory networks • lncRNA–miRNA–mRNA: Interactions, targeting, homology, integrated networks • circRNA–miRNA–mRNA: Source gene interaction, targeting, regulatory networks

Novogene Whole Transcriptome Sequencing Project Workflow

Final deliverables include publication‑ready analyses, figures, and summary reports. The flowsheet below illustrates the step‑by‑step WTS workflow.

Resources

1/1

Differential Gene Expression Statistics

Summarizes the number of up‑regulated and down‑regulated genes across each comparison group, providing an overview of expression changes between conditions.

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Interaction Analysis of Differential lncRNA Targets and mRNAs

Visualizes the relationships between differentially expressed lncRNA target genes and differentially expressed mRNAs. Categories include: up_mRNA, up_lncRNA_target, down_lncRNA_target, and down_mRNA.

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circRNA–miRNA–mRNA Triplet Counts and Networks

Identifies and quantifies circRNA–miRNA–mRNA regulatory triplets in which all three components are differentially expressed, and constructs interaction networks for each comparison group.

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GO Enrichment Analysis (Scatter Plot)

Frequently Asked Questions

What does Whole Transcriptome Sequencing (WTS) profile?

WTS captures all major RNA types, including mRNA, lncRNA, circRNA, miRNA, and other non coding RNAs, offering a complete and unbiased view of the transcriptome.

How is WTS different from mRNA seq or Total RNA seq?

What library types are used for WTS?

How much sequencing depth is recommended?

Can WTS identify novel RNA species?

What downstream analyses are included?

Does WTS support multi RNA regulatory network analysis?

Can WTS detect circRNAs?

What deliverables will I receive?

What sample types are accepted?

More Services

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