Our miRNA Sequencing and Analysis service delivers unbiased, genome-wide microRNA expression profiling across diverse sample types—including tissues, cells, and biofluids. Combining robust small RNA library construction, high-throughput Illumina sequencing, and a refined bioinformatics pipeline, we enable identification of known and novel miRNAs, differential expression analysis, and target prediction.
MicroRNAs (miRNAs) are key post-transcriptional regulators implicated in a wide range of diseases. Unlike qPCR arrays that target only known sequences, our sequencing-based approach provides an unbiased view of the entire miRNome, capturing isomiRs and novel species. Each project is scoped to your experimental design—from sample number and sequencing depth to validation strategies—ensuring results that directly support biomarker panels, mechanistic studies, or clinical candidate identification.
We accept a variety of input materials: total RNA, purified small RNA, or directly extracted biofluids (plasma, serum, urine, CSF). Standard library construction enriches small RNAs in the 18–30 nt range via 3′ and 5′ adapter ligation, followed by reverse transcription and limited-cycle PCR. Libraries are size-selected, QC-validated (Bioanalyzer, Qubit), and sequenced on Illumina platforms (typically single-end 50 bp). Our bioinformatics pipeline aligns reads to miRBase, quantifies known miRNAs, predicts novel candidates, and performs differential expression and target gene enrichment analysis.
Key Features
Wide Sample Compatibility
Total RNA, small RNA fractions, or direct input from biofluids (plasma, serum, urine, CSF) and solid tissues. RNA integrity and concentration are assessed prior to library preparation; minimum input requirements are scoped per project.
Robust Small RNA Library Construction
Library preparation uses 3′ and 5′ adapter ligation, reverse transcription, and PCR amplification with minimal cycles to preserve complexity. Size selection captures 18–30 nt inserts. Final libraries are quantified by Bioanalyzer and Qubit before sequencing.
High-Throughput Illumina Sequencing
Sequencing is performed on Illumina platforms (e.g., NextSeq 2000, NovaSeq 6000) with single-end 50 bp reads. Depth is tailored to project goals—typically 5–15 million reads per sample for discovery, or deeper for rare miRNA detection.
Comprehensive Bioinformatics Analysis
Our pipeline includes: adapter trimming, read alignment to miRBase (v22+), quantification of known miRNAs, prediction of novel miRNAs using miRDeep2 or equivalent, differential expression analysis (DESeq2/edgeR), and target prediction (miRDB, TargetScan). Results are delivered as an interactive report with tables, heatmaps, and PCA plots.
Applications & Modalities
Our miRNA sequencing service supports a broad range of research applications. Projects are customized to your biological question, sample type, and desired depth of analysis.
Biomarker Discovery: Identify differentially expressed miRNAs in disease versus control cohorts from biofluids or tissues. Suitable for early-phase biomarker panel development in oncology, neurodegeneration, cardiovascular disease, and infectious disease.
Mechanistic Studies: Profile miRNA expression changes upon drug treatment, genetic perturbation, or environmental exposure. Correlate miRNA signatures with mRNA expression or protein levels to build regulatory networks.
Extracellular Vesicle (EV) miRNA Analysis: Isolate and sequence miRNAs from exosomes and microvesicles. Enables non-invasive liquid biopsy profiling for disease monitoring and therapeutic response assessment.
Novel miRNA Discovery: Uncover previously unannotated miRNAs in your organism or tissue of interest. Pipeline includes miRDeep2 prediction, conservation analysis, and secondary structure validation.
Cross-Species Comparisons: Align reads to multiple miRBase species to identify conserved and species-specific miRNAs. Useful for evolutionary studies and model organism work.
Target Prediction & Pathway Analysis: Integrate differentially expressed miRNAs with predicted target genes and KEGG/GO enrichment to generate functional hypotheses for downstream validation.
Workflow
Each project follows a structured, consultative workflow—from initial scoping to final data delivery. Clear milestones and communication are maintained throughout.
Consultation & Experimental Design: Our scientific team reviews your sample types, number of samples, biological questions, and preferred sequencing depth. We provide a detailed project proposal with deliverables and timeline.
Sample QC & Library Construction: RNA integrity (RIN) and concentration are measured. Small RNA libraries are prepared with adapter ligation, RT, and limited-cycle PCR, followed by size selection (18–30 nt) and QC (Bioanalyzer, Qubit).
Illumina Sequencing: Libraries are normalized, pooled, and sequenced on an Illumina platform. Standard read length is single-end 50 bp; depth is set per project scope (typically 5–15 million reads per sample).
Bioinformatics Processing: Raw reads are demultiplexed, adapter-trimmed, and aligned to miRBase. Known and novel miRNAs are quantified. Differential expression analysis is performed using DESeq2 or edgeR with appropriate multiple-testing correction.
Delivery & Reporting: Final deliverables include: raw FASTQ files, expression matrices (counts and normalized), differential expression results, novel miRNA predictions, target gene lists, and a comprehensive analysis report (PDF/HTML) with figures and tables.
Customizable Scope
Sequencing depth, number of replicates, validation by qRT-PCR, and specific analysis requests (e.g., isomiR profiling, integrative analysis with mRNA-seq) are accommodated on a per-project basis. We also provide spike-in controls for absolute quantification when required.
Quality Assurance
Every project includes rigorous QC at multiple stages: RNA integrity assessment (RIN recommended for tissue/cell; biofluid samples evaluated for yield), library size distribution and concentration (Bioanalyzer trace), and sequencing quality metrics (Q30 ≥ 80%, read mapping rate). Adapter contamination is removed during preprocessing.
For differential expression, we apply appropriate normalization (TMM or quantile) and multiple-testing correction (Benjamini-Hochberg). All analysis scripts are reproducible, and raw data are archived for at least one year post-delivery.
Why Choose Us
End-to-End Service: From experimental design and library construction to advanced bioinformatics and reporting—we manage the entire workflow, reducing your project management burden.
Flexible Input & Depth: Accepts low-input biofluid samples as well as high-quality total RNA. Sequencing depth is tailored to discovery or targeted quantification needs.
Publication-Ready Reports: Deliverables include publication-quality figures (heatmaps, volcano plots, PCA) and tables suitable for supplementary files.
Experienced Bioinformatics Team: Our analysts have extensive experience with miRNA-seq data, including novel miRNA prediction, isomiR detection, and integrative multi-omics analysis.
Backed by Creative Biogene: All projects are delivered under Creative Biogene's ISO-aligned quality system, with dedicated project management, milestone-based reporting, and full intellectual property protection for your data.
Supported Sample Types
We accept a variety of sample formats. Optimal input quantities are determined during project scoping.
Biofluids (Plasma, Serum, Urine, CSF): Extracellular vesicle isolation or direct RNA extraction. Minimum volume depends on expected miRNA yield; typical inputs: 200–500 µL plasma/serum, 1–5 mL urine.
Tissues (Fresh-Frozen, FFPE): Total RNA extracted from solid tissues (e.g., tumor biopsies, brain regions, organoids). FFPE samples accepted with appropriate QC criteria.
Cultured Cells (Adherent, Suspension, Primary): Harvested cell pellets or RNA directly. Typical input: 10&sup5;–10&sup6; cells; lower inputs possible with specialized protocols.
Exosomes / Extracellular Vesicles: Pre-purified EV isolates or raw biofluid for on-site isolation. miRNA enrichment validated for low-yield EV samples.
Contact Us
Whether you are screening carriers, refining lead candidates, or building a regulatory package, the scientific team at Creative Biogene can help you design the right experimental strategy—from formulation and assay selection to data interpretation. Reach out to discuss a tailored solution for your next project.
