Whole Transcriptome Sequencing (WTS)

Whole Transcriptome Sequencing

Integrated RNA sequencing strategy for analysing coding RNA, long non-coding RNA, small RNA and circular RNA regulation.

Whole Transcriptome Sequencing provides an integrated view of multiple RNA types within the same study. By combining library strategies for coding transcripts, long non-coding RNAs, small RNAs and, where selected, circular RNAs, WTS supports broader analysis of transcriptome activity and RNA-mediated regulation.

Novogene Europe supports WTS projects using qualified total RNA inputs and library preparation options designed to capture different RNA classes. Bioinformatics workflows can support mRNA, lncRNA, miRNA and circRNA analysis, as well as differential expression, functional enrichment and regulatory network analysis across RNA types.

Service Highlights

Multi-library RNA Profiling

Combine library strategies for coding transcripts, long non-coding RNAs, small RNAs and circular RNAs to support broader transcriptome analysis.

Integrated RNA Type Analysis

Analyse mRNA, lncRNA, miRNA and circRNA expression within the same study to explore RNA-mediated regulation across multiple RNA classes.

Regulatory Network Insight

Bioinformatics workflows can support regulatory network analysis, including lncRNA–miRNA–mRNA and circRNA–miRNA–mRNA interaction models.

Flexible Study Design

Select library combinations based on project goals, RNA input quality and the level of coding, non-coding and regulatory RNA insight required.

Applications

Multi-layer Disease Research

Whole Transcriptome Sequencing can support studies of disease mechanisms by comparing coding, non-coding and regulatory RNA changes across sample groups or conditions.

Biomarker Discovery

Integrated RNA profiling can help identify candidate expression signatures across mRNA, lncRNA, miRNA and circRNA layers for biomarker-oriented research

ceRNA and Regulatory Network Research

WTS can support lncRNA–miRNA–mRNA and circRNA–miRNA–mRNA network analysis, helping researchers explore potential competing endogenous RNA regulation.

Treatment and Stress Response

Whole transcriptome data can help researchers explore RNA-level responses to treatment, infection, environmental stress or other biological challenges.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Library Type	Sample Type	Amount	RNA Integrity Number (Agilent 5400)	Purity (NanoDrop)
lncRNA Library & small RNA Library	Total RNA	≥ 1.5 μg	A≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
lncRNA library & small RNA library & circRNA library	Total RNA	≥ 2.5 μg	≥7.5, with flat baseline (animal) ≥7.0, with flat baseline (plant, fungus)	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

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);
Content of Data Analysis	Individual ncRNA analysis package Network analysis between lncRNA vs miRNA, mRNA vs miRNA, circRNA vs miRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA

Resources

Example Analysis Output

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Differential mRNA Summary

Summarise up- and down-regulated mRNA counts across selected comparison groups.

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lncRNA Target Overlap

Show overlap between differentially expressed mRNAs and predicted lncRNA target genes.

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circRNA–miRNA Network

Summarise circRNA, miRNA and gene counts in predicted regulatory network models.

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GO Enrichment Analysis

Identify enriched GO terms linked to differentially expressed genes for functional interpretation.

Webinars

Exploring the Untranslated — RNA Sequencing Basics & the Power of lncRNA

Looking to get started with RNA-seq or expand your transcriptomics research beyond protein-coding genes? Join this webinar to explore RNA-seq and lncRNA-seq technologies, learn when to include lncRNAs in your study, and gain practical guidance for designing successful transcriptomics projects.

Learn More

Frequently Asked Questions

How is WTS different from mRNA-seq?

mRNA-seq focuses on poly(A) for messenger RNA enrichment. WTS captures a broader range of RNA species by rRNA depletion and size selection. This supports integrated analysis of coding and non-coding RNA expression and regulatory interactions.

How is WTS different from Total RNA sequencing?

Which RNA can be analysed by WTS?

What research applications benefit most from WTS?

Does WTS support biomarker research?

Which sequencing strategies do WTS projects use?

Is bioinformatic analysis included with WTS?

What sample types are suitable for WTS?

Is WTS suitable for publication-driven studies?

Explore Transcriptomics Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

Have a project in mind?

Send us your enquiry and a Novogene Europe specialist will be in touch.

Explore Transcriptomics Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.