High-resolution, quantitative mRNA expression profiling from limited or challenging RNA samples for translational research.
Our transcriptome sequencing service delivers robust, quantitative gene expression data from total RNA or purified mRNA, supporting a wide range of sample types and experimental designs.
Whether your study involves scarce clinical biopsies, degraded RNA from FFPE tissues, or high-quality cell-line extracts, we provide end-to-end support from RNA extraction through bioinformatics interpretation. The service is designed for pharmaceutical R&D, biotech, and academic groups that require publication-ready expression data for oncology, neurology, ophthalmology, and other disease areas.
Our workflow employs polyA selection or ribosomal RNA depletion to enrich for mRNA, followed by strand-specific library preparation and high-throughput sequencing on Illumina platforms. A comprehensive bioinformatics pipeline performs read alignment, transcript quantification, and differential expression analysis, delivering results in a clear, interpretable format.
Key Features
RNA Quality Assessment
Total RNA is assessed for integrity (RIN or DV200) and purity using standard assays. Samples that do not meet minimum quality thresholds are flagged, and optional ribodepletion or polyA enrichment strategies are recommended based on RNA quality.
Library Preparation Options
We offer both polyA selection (for high-quality RNA) and ribosomal RNA depletion (for degraded or low-input RNA, including FFPE). Library preparation is strand-specific and can be configured for unstranded or stranded protocols, depending on your data requirements.
Flexible Sequencing Depth
Sequencing depth is scoped per project, typically ranging from 10 million to 100 million paired-end reads per sample. This flexibility accommodates both exploratory profiling and hypothesis-driven expression analysis.
Bioinformatics & Differential Expression
Our bioinformatics pipeline includes read alignment (STAR), transcript quantification (RSEM or Salmon), and differential expression analysis (DESeq2, edgeR). Results are delivered as raw FASTQ, aligned BAM, and normalized count matrices, along with a summary report.
Sequencing Modalities
We support multiple library preparation strategies to match your sample type and research question. Each modality is optimized to maximize transcript recovery and quantitative accuracy.
PolyA-Selected mRNA Sequencing: Enriches for polyadenylated transcripts, ideal for high-integrity RNA from cell lines or fresh-frozen tissues. Maximizes coverage of coding transcripts.
Ribo-depleted Total RNA Sequencing: Removes ribosomal RNA to capture both coding and non-coding transcripts. Recommended for degraded RNA, FFPE samples, or studies requiring long-noncoding RNA (lncRNA) detection.
Strand-Specific Sequencing: Preserves information on the transcribed strand, enabling accurate annotation of antisense transcription and gene overlap discrimination.
Low-Input RNA Sequencing: Optimized library preparation for samples with limited RNA amounts (down to 1–10 ng total RNA), using pre-amplification methods that maintain library complexity.
De Novo Transcriptome Assembly: For non-model organisms or species without a reference genome, we perform de novo assembly of transcripts using Trinity or similar tools, with annotation support.
Workflow
Each project follows a structured five-step workflow, from sample receipt through data delivery.
Sample QC and Project Confirmation: Total RNA or purified mRNA samples are received and assessed for quantity, purity, and integrity (RIN/DV200). Results are shared with you before proceeding to library preparation.
Library Preparation and Quality Control: Depending on the selected modality, mRNA is enriched via polyA capture or ribodepletion. Strand-specific libraries are constructed with adapters, barcoded, and amplified. Library quality is verified by Bioanalyzer or TapeStation.
High-Throughput Sequencing: Libraries are pooled and sequenced on an Illumina platform (NovaSeq or NextSeq) at the predetermined read depth, typically 50–150 bp paired-end. Real-time quality metrics are monitored during the run.
Bioinformatics Analysis: Primary analysis converts raw BCL files to FASTQ. Reads are aligned to the reference transcriptome (STAR), and transcript/gene expression is quantified using RSEM or Salmon. Quality control includes mapping rate, uniformity, and coverage statistics.
Data Delivery and Reporting: Deliverables include raw FASTQ files, aligned BAM files, a gene-level count matrix, and a differential expression report (if scoped). A project summary outlining key metrics is provided.
Quality Assurance
Every sample undergoes rigorous quality checks at multiple stages. RNA integrity is assessed using RIN or DV200 metrics and spectrophotometry. Library quality is verified by fragment analysis and qPCR quantification. Sequencing runs are monitored for cluster density, Q30 scores, and read distribution.
Bioinformatics quality control includes mapping rate, transcript coverage uniformity, and detection of potential contamination or batch effects. A comprehensive QC report is provided with every project deliverable to ensure data integrity and reproducibility. Total turnaround typically ranges from 6 to 8 weeks for standard projects; expedited timelines can be arranged upon request.
Why Choose Us
Flexible Library Prep: PolyA selection and ribodepletion options allow us to handle samples ranging from high-quality cell lines to challenging FFPE and low-input RNA.
End-to-End Bioinformatics: From raw reads to publication-ready expression tables, our bioinformatics pipeline provides alignment, quantification, and differential expression analysis.
Dedicated Project Management: A named scientific contact coordinates your project from start to finish, with milestone updates and responsive support.
Transparent Reporting: We deliver detailed QC reports alongside your data, so you have full visibility into data quality at every stage.
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
Our transcriptome sequencing service is compatible with a broad range of sample types, including those with limited or degraded RNA. Common sample categories include:
Fresh-Frozen Tissues: High-quality RNA from solid tissues (e.g., tumor biopsies, xenografts, organ samples).
FFPE Tissues: Formalin-fixed, paraffin-embedded clinical samples, processed using ribodepletion and low-input protocols.
Cell Lines & Primary Cells: Cultured cells, iPSCs, and primary cells from various species, with optional polyA or ribodepletion.
Blood & Circulating RNA: Total RNA from whole blood, buffy coat, or plasma (for exosomal RNA studies).
Contact Us
Whether you are profiling expression in scarce clinical samples, comparing treatment groups, or building a publication-ready dataset, the scientific team at Creative Biogene can help you design the right sequencing strategy—from library preparation through bioinformatics interpretation. Reach out to discuss a tailored solution for your next project.
