Total RNA Sequencing Services

Total RNA Sequencing

rRNA-depleted transcriptome sequencing for profiling coding RNA and long non-coding RNA across biological samples and conditions.

Total RNA sequencing, also known as Total RNA-seq, uses ribosomal RNA depletion to profile a broader transcriptome than poly(A)-selected mRNA-seq. This approach captures both messenger RNA and long non-coding RNA, supporting analysis of gene expression, transcript diversity and regulatory RNA activity across biological conditions.

Novogene Europe supports rRNA-depleted Total RNA-seq projects with high-throughput sequencing and bioinformatics workflows for expression quantification, differential expression analysis, lncRNA identification, functional enrichment and regulatory interpretation. The service is suitable for researchers who want to study coding and long non-coding transcript changes within the same RNA-seq experiment.

Service Highlights

rRNA-depleted Transcriptome Profiling

Use ribosomal RNA depletion to profile coding transcripts and long non-coding RNAs within the same RNA-seq experiment, supporting broader transcriptome analysis.

Coding and lncRNA Analysis

Analyse both mRNA and lncRNA expression to explore transcriptome regulation, expression changes and coding–non-coding RNA relationships.

Expression and Functional Analysis

Bioinformatics workflows support expression quantification, differential expression analysis, functional enrichment and pathway-level interpretation.

Regulatory Target Insight

lncRNA target prediction and regulatory analysis can support investigation of potential relationships between long non-coding RNAs and gene expression changes.

Applications

Coding and Non-coding RNA Regulation

Total RNA-seq helps researchers study mRNA and lncRNA expression together, supporting investigation of coding–non-coding RNA regulation across biological conditions.

Disease and Treatment Response Research

rRNA-depleted RNA-seq can support studies of disease mechanisms, treatment response and biological change by comparing transcript profiles across sample groups.

lncRNA Discovery and Functional Insight

Total RNA-seq supports identification and analysis of long non-coding RNAs, helping researchers explore their potential roles in gene regulation and cellular processes.

Pathway and Regulatory Network Analysis

Transcriptome data can be used to investigate affected pathways, regulatory relationships and biological processes linked to differential RNA expression.

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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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	Purity (NanoDrop)
lncRNA Library	Total RNA	≥ 300 ng	≥5.5, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Exosomal lncRNA Library	Exosomal RNA	≥ 5 ng	Fragments between 25-200nt, FU*>10, with flat baseline	OD260/280≥2.0. OD260/230≥2.0. no degradation, no contamination
Dual RNA library	Total RNA	≥ 1 μg	≥ 6.5, with flat base line	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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

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
Recommended Data Output	≥ 40 million read pairs per sample
Recommended Sequencing Depth	≥ 40 million read pairs per sample for species with reference genome
Standard Data Analysis	Data Quality ControlStructural Analysis (Alternative Splicing & Variation Calling)lncRNA Identification & AnnotationExpression Quantification & Differential Expression ProfilingFunctional Enrichment AnalysisProtein-Protein Interaction (PPI) analysislncRNA Target Gene Prediction

Resources

Example Analysis Output

1/1

lncRNA Coding Potential

Identify candidate lncRNAs by integrating coding-potential assessment across multiple prediction tools.

1/1

lncRNA Feature Comparison

Compare transcript features such as length and expression patterns between lncRNAs and mRNAs.

1/1

Expression Distribution

Review expression level distributions across samples to assess overall RNA abundance profiles and consistency.

1/1

Expression Volcano Plot

Highlight significantly changed genes or transcripts based on fold change and statistical significance.

1/1

Expression Heatmap

Visualise differential expression patterns across samples and experimental groups.

Webinars

ncRNA-seq Results Explained: What you can explore with non-coding RNA data

Learn how to navigate and interpret non-coding RNA sequencing (ncRNA-seq) data, including lncRNA-seq, small RNA-seq, and circRNA-seq. This webinar will provide an overview of analysis workflows, data visualisation approaches, and the tools needed to transform complex datasets into meaningful biological insights.

Learn More

Frequently Asked Questions

How does Total RNA-seq differ from mRNA-seq?

mRNA-seq usually targets poly(A)+ transcripts and primarily profiles protein-coding transcripts. In contrast, Total RNA-seq removes rRNA to capture both coding and non-coding RNAs. This method allows for a wider analysis of the transcriptome.

What research applications benefit most from Total RNA-seq?

Can researchers use Total RNA-seq for lncRNA analysis?

Which library preparation strategy does Novogene use for Total RNA-seq?

Is strand information preserved in Total RNA-seq?

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.