Prokaryotic RNA Sequencing Services

Prokaryotic RNA Sequencing

Strand-specific RNA sequencing for profiling gene expression, operon structure and regulatory responses in bacteria and archaea.

Prokaryotic RNA sequencing enables transcriptome-wide analysis of RNA expression in bacteria, archaea and other prokaryotic systems. Using strand-specific RNA-seq, this approach supports accurate gene expression profiling and helps researchers investigate transcriptional activity, operon organisation and condition-specific regulatory responses.

Novogene Europe supports Prokaryotic RNA-seq projects using high-throughput short-read sequencing and bioinformatics workflows for expression quantification, differential expression analysis, enrichment analysis and prokaryote-specific transcriptome interpretation. Analysis options can include novel transcript prediction, operon prediction, promoter and transcription start site/transcription termination site (TSS/TTS) analysis, Shine-Dalgarno sequence prediction, terminator prediction and small RNA target analysis.

Service Highlights

Strand-specific Expression Profiling

Profile prokaryotic RNA expression with strand-specific sequencing to support accurate gene-level analysis, transcriptome-wide comparison and regulatory interpretation.

Operon and Transcript Structure Insight

Bioinformatics workflows can support operon prediction, promoter analysis and TSS/TTS identification to help interpret prokaryotic transcription organisation.

Differential and Functional Analysis

Compare RNA expression across sample groups and explore enriched pathways or biological functions linked to differentially expressed genes.

Regulatory RNA Analysis

Analysis options can support novel transcript prediction, small RNA target analysis, Shine-Dalgarno sequence prediction and terminator prediction.

Applications

Microbial Stress Response

Prokaryotic RNA-seq can help investigate how bacteria or archaea respond to stress, nutrient changes, environmental shifts or experimental treatments.

Antimicrobial Response Research

Transcriptome profiling supports studies of microbial responses to antibiotics, antimicrobial compounds or resistance-related experimental conditions.

Host–Microbe Interaction

RNA expression data can help explore microbial activity in host-associated environments, infection models or host–microbe interaction studies.

Metabolic and Functional Adaptation

Prokaryotic RNA-seq supports research into metabolic pathways, functional adaptation and condition-specific microbial behaviour across study groups.

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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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
Prokaryotic RNA Library	Total RNA	≥ 300 ng	≥ 6.0, 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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

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 Sequencing System
Read Length	Paired-end 150bp
Recommended Data Amount	≥ 2Gb raw data per sample for the species with reference genome
Content of Data Analysis	Data Quality Control Alignment to Reference Genome Gene Expression Analysis Novel Transcript Prediction Gene expression quantification & Differential expression analysis Enrichment Analysis Operon, Promoter and TSS/TTS Prediction SD Sequence Prediction Rho-independent Terminator Sequence Prediction sRNA Secondary Structure Prediction sRNA Targeted Gene Prediction, etc.

Resources

Example Analysis Output

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Sample Correlation

Review pairwise correlation between samples to assess expression similarity and data consistency.

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Sample PCA

Visualise sample clustering and group separation based on transcriptome-wide expression profiles.

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Differential Gene Overlap

Show shared and unique differentially expressed genes across comparison groups.

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Expression Volcano Plot

Highlight significantly up- and down-regulated genes based on fold change and statistical significance.

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Expression Heatmap

Visualise differential gene expression patterns across samples and experimental groups.

Webinars

Unfolding the Microbial World: A Journey through Sequencing Applications

Explore the latest microbial sequencing approaches, including microbial whole genome sequencing, metagenomics, and metatranscriptomics, and learn how advances such as long-read sequencing are expanding our understanding of microbial communities and ecosystems.

Learn More

Explore Transcriptomics Insights

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

Speak with a Specialist

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