Sample Submission Guidelines
Our Capabilities in IVT mRNA Sequencing
Our Capabilities in IVT mRNA Sequencing
- Comprehensive mRNA Analysis
Our IVT mRNA sequencing service provides a detailed analysis of your mRNA samples, covering key factors essential for accurate assessment and research insights. - mRNA Integrity: We ensure that the mRNA is intact, free from degradation products, and maintains its structural integrity.
- Full-length Sequencing: By sequencing the entire mRNA length, we provide a complete view of its sequence, including critical regions such as the 5' cap and 3' poly(A) tail. This ensures no data is missed in the analysis.
- Poly(A) Tail Length: The poly(A) tail influences mRNA stability and translation. We provide precise measurements to assess mRNA functional quality.
- Sequence Identity: Our service guarantees that the mRNA matches the expected sequence, confirming that the transcription process generated the correct RNA molecule.
- Contamination Detection: We check for contaminants like plasmid DNA, rRNA, or other unwanted RNA sequences, ensuring your mRNA sample is pure and suitable for downstream applications.
Customization for Your Needs
We understand that each research project has unique needs. Our IVT mRNA sequencing solutions can be customized to support various applications:
- mRNA Vaccine Development: Ensure the quality of your mRNA vaccine candidate with detailed sequence integrity and poly(A) tail analysis.
- RNA Therapeutics Research: Evaluate the quality and functionality of therapeutic mRNA, ensuring your RNA-based treatments are effective and safe.
- Gene Expression Studies: Gain reliable data for transcript analysis in gene expression research, investigating RNA regulation and splicing.
We tailor our services to meet the specific demands of your project, providing you with the most relevant and actionable data.
Our IVT mRNA Sequencing Technology Package
Our IVT mRNA sequencing service leverages the latest advancements in both sequencing technology and computational analysis. This comprehensive package provides a complete solution for evaluating the quality of mRNA samples, focusing on sequencing accuracy, contamination detection, and functional analysis. Here's a breakdown of the key components of our technology package:
| Component | Description |
|---|---|
| IVT mRNA Purification | High-quality purification to remove contaminants like plasmid DNA and rRNA, ensuring only intact mRNA is analyzed for accurate sequencing. |
| Sequencing Platforms | - Oxford Nanopore: Long-read sequencing for full-length mRNA analysis. - Illumina: High-accuracy short-read sequencing for comprehensive mRNA analysis. |
| Bioinformatics Analysis | Expert analysis of sequencing data, including: - mRNA integrity and sequence identity verification - Detection of contaminants (rRNA, plasmid DNA) - Poly(A) tail length analysis |
| Technology Advantage | The combined use of advanced long-read and short-read platforms ensures the most reliable and detailed mRNA analysis, backed by expert bioinformatics support for actionable results. |
IVT mRNA Sequencing Workflow
Our IVT mRNA sequencing workflow is designed to provide a seamless, end-to-end solution for mRNA quality analysis. Each step is optimized to ensure that you receive the most accurate and reliable data for your research needs.
- Sample Preparation
High-quality IVT mRNA samples are prepared for sequencing. This step involves receiving purified mRNA or cDNA clones from your lab, ensuring that the samples are free from contaminants that could affect the sequencing process. - Sequencing
Using Illumina and Oxford Nanopore sequencing platforms, the prepared mRNA samples are sequenced. The sequencing process provides high-accuracy data, enabling detailed analysis of the full mRNA transcript, including the 5' cap and poly(A) tail. - Bioinformatics Analysis
After sequencing, our bioinformatics team performs a comprehensive analysis of the data. This includes:- Assessing mRNA integrity: Verifying that the mRNA is intact and free from degradation.
- Sequence identity verification: Confirming that the mRNA matches the expected sequence.
- Contamination detection: Identifying any potential contaminants, such as rRNA or plasmid DNA.
- Deliverables
You will receive a detailed report that includes:- mRNA quality metrics: Sequence integrity, poly(A) tail length, and contamination levels.
- Sequencing readouts: Full data files, including alignment files and coverage plots, for further analysis.
Sequencing Platforms
Oxford Nanopore Technologies
Oxford Nanopore is a leader in long-read sequencing technology, making it ideal for mRNA sequencing. Unlike short-read technologies, Oxford Nanopore's long-read platform allows for the sequencing of full-length mRNA molecules, capturing key elements such as:
- The 5' cap region
- The coding sequence
- The 3' poly(A) tail
This capability is particularly important for obtaining a complete and accurate representation of the mRNA sequence. Long-read sequencing provides deeper insights into the mRNA's integrity, functional elements, and potential splice variants.
Key Benefits:
- Full-length sequencing of mRNA
- High accuracy for mRNA integrity analysis
- Ideal for detecting poly(A) tail length and sequence features
Illumina Sequencing
Illumina is known for its high-throughput, short-read sequencing capabilities, providing high accuracy and sensitivity in sequencing. This platform is widely used for large-scale RNA sequencing and is well-suited for:
- High-coverage sequencing of mRNA transcripts
- Large-scale data generation for gene expression studies
Providing reliable data for quantitative analysis of mRNA levels across multiple samples
Why We Use Both Platforms
By combining Oxford Nanopore and Illumina platforms, we ensure that your IVT mRNA sequencing results are as accurate and comprehensive as possible:
- Oxford Nanopore offers full-length sequencing and deeper insights into mRNA structure.
- Illumina delivers high-quality data with high coverage for in-depth gene expression analysis.
This dual-platform approach guarantees that we provide you with both the depth and breadth of data necessary for advanced mRNA research, including the detection of sequence variants, functional elements, and contamination.
Bioinformatics Analysis
At CD Genomics, we provide a comprehensive bioinformatics analysis as part of our IVT mRNA sequencing service. Our team of experts leverages advanced computational tools to ensure that you receive detailed, meaningful insights from your sequencing data. This analysis is crucial for making informed decisions in your research and further optimizing your mRNA development.
- Quality Control
- Sequence Integrity: We assess the integrity of the mRNA by checking for any degradation or errors in the sequence. This ensures that the mRNA is intact and accurately reflects the intended transcript.
- Poly(A) Tail Length: We accurately measure the length of the poly(A) tail, which is essential for mRNA stability and translation efficiency.
- Alignment to Reference
- Read Alignment: Our analysis involves aligning the sequencing reads to a reference genome or transcriptome to confirm the sequence identity. This step ensures that your mRNA sequence matches the expected design, and identifies any sequence variations or errors.
- Contamination Detection
- Contaminant Identification: We identify and quantify any contaminants (e.g., rRNA, plasmid DNA, or other RNA species) that could compromise the data quality. This step is essential for ensuring the purity of your mRNA sample.
- Data Filtering: Contaminants are removed from the dataset, ensuring that only relevant mRNA sequences are included in the analysis.
- Functional Analysis
- Gene Expression Analysis: We provide a detailed analysis of gene expression levels, which is essential for studying mRNA transcription and regulation.
- Splice Variant Detection: We analyze the sequencing data for potential splice variants, which could impact mRNA functionality. This step is crucial for understanding how alternative splicing might influence the mRNA's role in various applications.
We understand that every research project has unique needs. Our bioinformatics team works closely with you to tailor the analysis to your specific goals, ensuring that the results are relevant and actionable for your research.
Why Choose CD Genomics for IVT mRNA Sequencing?
- Expertise and Innovation: Over a decade of experience in RNA sequencing and mRNA analysis.
- Advanced Technology: Dual-platform approach using Illumina and Oxford Nanopore for comprehensive sequencing.
- Tailored Solutions: Customized services for mRNA vaccine, RNA therapeutics, and gene expression research.
- Reliability and Quality: High-quality, reproducible data with stringent quality control.
- Timely Delivery: Fast turnaround times to meet your research deadlines.
Sample Requirements
| Sample Type | Description | Preferred Methods | Quantity Requirements | Storage & Shipping |
|---|---|---|---|---|
| Purified mRNA | Free of contaminants like genomic DNA and rRNA. | PolyA selection or rRNA depletion for purification. | 500 ng to 1 µg per sample. | Store at -80°C, ship on dry ice or cold packs. |
| cDNA Clones | High-quality plasmid DNA with full-length cDNA of the gene of interest. | Ensure high-quality plasmid prep for IVT synthesis. | At least 100 ng of plasmid DNA. | Store at -80°C, ship on dry ice or cold packs. |
| Sample Condition | Samples must be intact and free from degradation. | Avoid RNase contamination to preserve RNA integrity. | N/A | Samples should remain frozen during shipping. |
Deliverables
- mRNA Sequence Report: Includes integrity, poly(A) tail length, and contamination levels.
- Raw Data Files: FastQ files, alignment files, and coverage plots.
- Bioinformatics Analysis: Includes sequence alignment, contamination detection, and functional analysis.
- Data Visualization: Interactive plots for easy interpretation of results.
As part of the demo results, we provide:
Sequencing Coverage Plots: Visual representations of sequencing data, showing coverage uniformity and integrity.
Poly(A) Tail Length Analysis: Detailed charts showing accurate poly(A) tail measurement.
Contamination Reports: Clear reports highlighting any contaminants in the sample, with suggestions for purification.
FAQs
What is IVT mRNA sequencing?
IVT mRNA sequencing is a method used to analyze the sequence and quality of mRNA molecules synthesized in vitro. It allows for the comprehensive study of mRNA integrity, poly(A) tail length, sequence identity, and contamination levels, which is critical for mRNA vaccine development, RNA therapeutics, and gene expression research.
Why is mRNA vaccine quality analysis important?
Ensuring the quality and integrity of mRNA is crucial for the effectiveness and safety of mRNA vaccines. IVT mRNA sequencing provides detailed insights into the mRNA's sequence, structural integrity, and contamination levels, helping researchers identify potential issues before advancing to further stages of vaccine development.
How does IVT mRNA synthesis work?
In IVT mRNA synthesis, cDNA is transcribed into mRNA using an in vitro transcription (IVT) system. The resulting mRNA is purified and then analyzed through sequencing to assess its quality. This process is essential for producing high-quality mRNA that meets the specifications required for research and therapeutic applications.
What types of samples can I submit for sequencing?
We accept both purified mRNA and cDNA clones for sequencing. Purified mRNA should be free of contaminants like rRNA and genomic DNA, while cDNA clones should be of high quality and contain full-length transcripts of the gene of interest. Refer to our Sample Requirements section for more detailed instructions.
How long does it take to get results from IVT mRNA sequencing?
The turnaround time for IVT mRNA sequencing can vary depending on the complexity of the sample and the analysis required. On average, you can expect results within several weeks after receiving your samples. We also provide updates throughout the process to ensure transparency and timely communication.
Do you provide bioinformatics analysis with the sequencing data?
Yes, our bioinformatics analysis is an integral part of the IVT mRNA sequencing service. We provide comprehensive data analysis, including alignment to a reference genome, mRNA integrity checking, poly(A) tail analysis, contamination detection, and functional analysis, all included in the final report.
What if I need the data sooner?
If you require a faster turnaround, we offer expedited services. Please contact our customer support team before submitting your samples to discuss options and pricing for faster processing.
Can you help with experimental design for my project?
While we specialize in sequencing and bioinformatics analysis, our team can provide guidance on best practices for mRNA synthesis, purification, and experimental setup to ensure your samples are optimized for sequencing.
Are your services suitable for large-scale projects?
Absolutely! Our sequencing platforms are capable of handling high-throughput sequencing for large-scale projects, ensuring that we can support both small and large research teams or pharma companies.
Do you provide data in a format that's easy to use?
Yes! We provide all sequencing data in standardized file formats such as FastQ and BAM for seamless integration with other analysis tools. Our reports are also available in PDF format, with interactive visualizations to help you easily interpret your results.
References:
- Gunter, H.M., Idrisoglu, S., Singh, S. et al. mRNA vaccine quality analysis using RNA sequencing. Nat Commun 14, 5663 (2023). https://doi.org/10.1038/s41467-023-41354-y
- Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30;15(6):R86. DOI: 10.1186/gb-2014-15-6-r86
