N2Jenomics Lab Pvt. Ltd. provides comprehensive Small RNA Sequencing services for the identification, quantification, and characterization of small non-coding RNAs. Our optimized library preparation, high-throughput sequencing, and advanced bioinformatics enable accurate profiling of known and novel small RNAs to support gene regulation, biomarker discovery, and functional genomics research.

What Is Small RNA Sequencing?

Small RNA sequencing is a next-generation sequencing (NGS) approach used to profile small non-coding RNAs (typically <200 nucleotides) that regulate gene expression at the post-transcriptional level.

Major classes of small RNAs include:

• • MicroRNAs (miRNAs)

• • Small interfering RNAs (siRNAs)
• • PIWI-interacting RNAs (piRNAs)
• • Small nucleolar RNAs (snoRNAs)
• • Small nuclear RNAs (snRNAs)

These RNA molecules play essential roles in RNA silencing, gene regulation, cell differentiation, development, immune responses, apoptosis, and disease progression.

Using high-throughput sequencing, researchers can accurately identify known and novel small RNAs, quantify their expression levels, detect sequence variants, and investigate their biological functions across diverse sample types.

Advantages of Our Small RNA Sequencing Service

• Comprehensive Small RNA Profiling

Simultaneously profiles multiple classes of small non-coding RNAs, including miRNAs, siRNAs, piRNAs, snoRNAs, and snRNAs.

• Novel Small RNA Discovery

Identifies previously uncharacterized small RNAs, sequence variants (isomiRs), and potential biomarkers.

• High Sensitivity & Accuracy

Detects low-abundance transcripts with single-nucleotide resolution and provides accurate expression quantification over a broad dynamic range.

• High-Throughput Sequencing

Generates millions of high-quality sequencing reads for robust small RNA expression analysis.

• Advanced Bioinformatics

Comprehensive analysis includes expression profiling, differential expression, target prediction, and functional enrichment.

• Customized Experimental Design

Flexible workflows optimized for different organisms, sample types, and research objectives.

• Expert Technical Support

Our experienced scientists provide guidance on experimental design, sequencing strategy, and biological interpretation.

Applications

Small RNA sequencing is widely used for:

• • miRNA expression profiling
• • Novel small RNA discovery
• • Biomarker identification
• • Cancer research
• • Developmental biology
• • Plant and agricultural research
• • Neuroscience
• • Immunology
• • Epigenetics
• • Functional genomics
• • Precision medicine

Small RNA Sequencing Workflow

1. RNA Extraction

Isolation of high-quality total RNA followed by enrichment of the small RNA fraction.

2. Library Preparation

Adapter ligation, reverse transcription, PCR amplification, and library quality assessment optimized for small RNA molecules.

3. High-Throughput Sequencing

Sequencing performed on advanced Illumina platforms to generate high-quality small RNA datasets.

4. Bioinformatics Analysis

Comprehensive downstream analysis including:

• • Raw data quality control
• • Adapter trimming and filtering
• • Read alignment
• • Known small RNA annotation
• • Novel small RNA prediction
• • miRNA/isomiR identification
• • Differential expression analysis
• • Target gene prediction
• • GO enrichment analysis
• • KEGG pathway analysis
• • Functional annotation

Service Specification

	Sample Requirements Total RNA ≥ 1 μg, Minimum Quantity: 200 ng, Concentration≥ 20 ng/µl Cells≥ 2×106 Tissue ≥ 500 mg, Minimum Quantity: 100 mg OD A260/A280 ratio ≥ 1.8, A260/230 ratio≥ 1.8, RIN ≥ 6 All total RNA samples should be DNA-free RNA should be stored in nuclease-free water or RNA Stable. Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
	Sequencing Strategies Libraries of miRNA (15-30nt), small RNA (30-200nt), or custom size range Illumina HiSeq SE50 ≥ 10 M reads More than 90% of bases with a ≥Q30 quality score
	Data Analysis We provide multiple customized bioinformatics analyses: Raw data quality control and length filter Reference-based mapping Small RNA classification and quantification Target gene prediction and annotation Novel small RNA prediction Target gene analysis of differentially expressed small RNA (GO enrichment and KEGG enrichment) Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in Small RNA Sequencing for your writing (customization)

1. What does the data preprocessing workflow include?

Our bioinformatics pipeline begins with adapter trimming and quality filtering, followed by optional error correction when appropriate. Clean reads are then aligned to the reference genome or small RNA databases for annotation and quantification. Normalization is performed to minimize differences in sequencing depth across samples before downstream analyses.

2. How much sequencing depth is recommended?

The required sequencing depth depends on your research objective:

• cExpression profiling: Approximately 0.1–2 million mapped reads per sample is generally sufficient.

• • Novel small RNA discovery: 5–10 million reads or more per sample is recommended to maximize sensitivity.

Our team can recommend the optimal sequencing depth based on your study design.

3. How many biological replicates should I include?

To improve statistical power and reduce biological variability, we recommend at least three biological replicates per experimental group. The optimal number of replicates may vary depending on the study objectives and experimental design.

4. How should I ship my samples?

RNA samples should be shipped on dry ice or preserved using an RNA stabilization reagent according to the sample type. Frozen cell pellets and tissue samples should also be transported on dry ice to maintain RNA integrity during shipment.

5. What sample types are accepted?

We accept a wide variety of sample types, including:

• • Total RNA
• • Cultured cell pellets
• • Tissue samples
• • Bacterial cell pellets (including E. coli)
• • Other biological samples suitable for small RNA extraction

If you are unsure whether your samples are suitable, our technical team can provide guidance before shipment.

6. Is poly(A) enrichment or rRNA depletion required for miRNA sequencing?

No. Standard small RNA library preparation selectively captures small RNA molecules through adapter ligation, so poly(A) enrichment and rRNA depletion are generally not required for microRNA sequencing.

7. Why can't I open the downloaded FASTQ files?

FASTQ files are often very large and are typically compressed. If you cannot open them:

• • Ensure the files are fully downloaded and decompressed (if applicable).
• • Use bioinformatics tools or text editors capable of handling large files.
• • Linux systems or dedicated FASTQ viewers are generally recommended for efficient file access and analysis.