RNA Sequencing (RNA-Seq) & Transcriptome Analysis

Comprehensive Transcriptome Profiling for Accurate Gene Expression and Functional Genomics

Unlock the complexity of the transcriptome with N2Jenomics Lab's end-to-end RNA Sequencing services. Using advanced Illumina and long-read sequencing technologies, we provide high-resolution insights into gene expression, transcript diversity, alternative splicing, fusion transcripts, non-coding RNAs, and regulatory pathways. Our integrated wet-lab and bioinformatics workflow delivers publication-ready data for researchers working across plants, animals, microbes, and human research.

What is RNA Sequencing?

RNA Sequencing (RNA-Seq) is a powerful next-generation sequencing (NGS) technology that enables comprehensive analysis of all RNA molecules expressed within a biological sample. Unlike traditional expression profiling methods, RNA-Seq offers unbiased, genome-wide detection of coding and non-coding transcripts while simultaneously identifying novel genes, splice variants, fusion transcripts, and sequence variations.

Transcriptome sequencing enables researchers to understand how genes are regulated across developmental stages, environmental conditions, disease progression, or experimental treatments, making it one of the most widely used technologies in functional genomics and molecular biology.

Why Choose RNA-Seq?

Our RNA-Seq platform provides researchers with comprehensive transcriptome information to answer a wide range of biological questions.

Key Benefits

•  

• •  Genome-wide gene expression profiling

• •  Differential gene expression (DEG) analysis

• •  Discovery of novel transcripts

• •  Alternative splicing analysis

• •  Fusion transcript detection

• •  SNP and InDel identification from expressed genes

• •  Long non-coding RNA (lncRNA) discovery

• •  Functional pathway and enrichment analysis

• •  Biomarker identification

• •  Comparative transcriptomics across multiple conditions

Our RNA-Seq Workflow

1. Experimental Design

Our experts assist in selecting the most appropriate sequencing strategy, sample size, sequencing depth, and biological replicates based on your research objectives.

2. RNA Quality Assessment

High-quality RNA is evaluated for purity, integrity, and concentration using standardized quality control procedures before library preparation.

3. Library Preparation

Customized library construction options include:

•  

• •  Poly(A) mRNA Enrichment

• •  Total RNA with rRNA Depletion

• •  Strand-Specific RNA Libraries

• •  Small RNA Libraries

• •  Long-Read Isoform Libraries

4. High-Throughput Sequencing

We utilize industry-leading sequencing platforms including:

• •  Illumina NovaSeq

• •  Illumina NextSeq

• •  PacBio Iso-Seq

• •  Oxford Nanopore Technologies (ONT)

5. Bioinformatics Analysis

Our experienced bioinformatics team performs comprehensive downstream analysis including:

•  

• •  Raw data quality assessment

• •  Adapter trimming and filtering

• •  Genome alignment or de novo transcriptome assembly

• •  Transcript quantification

• •  Differential expression analysis

• •  Functional annotation

• •  GO enrichment

• •  KEGG pathway analysis

• •  Alternative splicing analysis

• •  Novel transcript discovery

• •  Gene fusion analysis

• •  SNP and InDel detection

• •  Publication-ready visualization

RNA Sequencing Services

mRNA Sequencing

Ideal for quantitative gene expression analysis and differential expression studies using poly(A)-enriched RNA libraries.

Applications

•  

• •  Gene expression profiling

• •  Disease mechanism studies

• •  Drug response analysis

• •  Biomarker discovery

Total RNA Sequencing

Provides comprehensive transcriptome coverage by capturing both coding and non-coding RNA populations after ribosomal RNA depletion.

Applications

•  

• •  lncRNA research

• •  Regulatory RNA studies

• •  Comprehensive transcriptome profiling

• •  Degraded RNA samples

Full-Length Transcript Sequencing (Iso-Seq)

Long-read sequencing enables complete characterization of transcript isoforms without transcript assembly.

Applications

•  

• •  Alternative splicing

• •  Isoform discovery

• •  Transcript annotation

• •  Fusion gene analysis

Bioinformatics Deliverables

Every RNA-Seq project includes a comprehensive analysis package.

Standard Deliverables

•  

• •  Raw FASTQ files

• •  Quality Control Report

• •  Clean sequencing reads

• •  Alignment statistics

• •  Gene expression matrix

• •  Differential expression analysis

• •  Volcano plots

• •  Heatmaps

• •  PCA analysis

• •  Hierarchical clustering

• •  GO Enrichment Analysis

• •  KEGG Pathway Analysis

• •  Publication-ready figures

• •  Complete bioinformatics report

Optional analyses can include:

•  

• •  WGCNA

• •  Time-series analysis

• •  Alternative splicing

• •  Fusion transcript detection

• •  Variant calling

• •  eQTL analysis

• •  De novo transcriptome assembly

Applications of RNA-Seq

Our transcriptome sequencing services support research across diverse scientific disciplines.

•  

• •  Functional Genomics

• •  Plant Biology

• •  Crop Improvement

• •  Cancer Research

• •  Developmental Biology

• •  Immunology

• •  Neuroscience

• •  Microbial Transcriptomics

• •  Host–Pathogen Interaction

• •  Drug Discovery

• •  Precision Medicine

• •  Biomarker Discovery

• •  Comparative Transcriptomics

• •  Systems Biology

Why N2Jenomics Lab?

At N2Jenomics Lab, we combine advanced sequencing technologies with robust bioinformatics expertise to deliver reliable and publication-ready transcriptomic datasets. Our experienced scientific team supports projects from experimental planning through data interpretation, ensuring high-quality results tailored to your research goals.

Our Advantages

•  

• •  End-to-end RNA-Seq workflow

• •  Customized experimental design

• •  Multi-platform sequencing capability

• •  Advanced bioinformatics support

• •  Fast turnaround time

• •  Publication-ready reports

• •  Dedicated project management

• •  Support for all organisms

• •  Flexible analysis pipelines

• •  Scalable solutions for academic and industrial research

•  

Frequently Asked Questions

Which organisms do you support?

We provide RNA-Seq services for plants, animals, microorganisms, fungi, and other research organisms.

Can you perform de novo transcriptome assembly?

Yes. We support both reference-guided and de novo transcriptome assembly depending on genome availability.

What sequencing depth should I choose?

Sequencing depth depends on project objectives, organism complexity, and the desired biological resolution. Our scientists help determine the optimal sequencing strategy during project planning.

Do you provide bioinformatics analysis?

Yes. Comprehensive bioinformatics analysis and publication-ready reports are included, with additional customized analyses available upon request.

What file formats will I receive?

Typical deliverables include FASTQ files, expression matrices, differential expression results, QC reports, functional annotations, pathway analyses, and publication-quality visualizations.