RNA sequencing (RNA-seq): Access the gene expression information
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Highlights
Explore the transcriptome by analyzing gene expression, detect novel transcripts and drive breakthroughs with RNA-seq. Lear how MGI tech platforms, library prep kits and automation solutions can streamline your RNA-seq workflow for high-quality, accurate data.
Introduction
RNA Sequencing (RNA-seq) is a powerful method that leverages next-generation sequencing (NGS) technology to analyze and quantify the diverse population of RNA molecules in a given biological sample, or at single-cell level. By examining the transcriptome—the total set of RNA transcripts, including mRNA, rRNA, tRNA, and various non-coding RNAs—researchers gain a dynamic view of gene expression and regulatory mechanisms at a specific point in time.
What Is RNA Sequencing?
RNA Sequencing (RNA-seq) is the NGS method dedicated to analyse the transcriptome, providing information related to the gene expression, but RNA-seq also enable o access information related to alternative splicing, gene fusions, transcripts orientation and isoforms expression.. Unlike DNA sequencing, which provides a static snapshot of the genome, RNA-seq can delivers a dynamic view of gene expression patterns. Compare to PCR or microarray technologie RNA-seq enables researchers to quantify the expression of thousands of genes simultaneously.
MGI Sequencing Platforms for RNA-seq
DNBSEQ-G400 Offers flexible throughput, ideal for mid- to high-throughput RNA-seq projects.
DNBSEQ-T7: Delivers very high throughput, ideal for large-scale studies like population-level transcriptomics.
DNBSEQ-E25: A more compact system designed for lower- to mid-range throughput, perfect for smaller labs or targeted RNA-seq.
Each MGI platform utilizes DNB Technology——which ensures high accuracy and low error rates critical for transcriptome studies.
Key Benefits of RNA-Seq
1. Comprehensive Analysis
RNA-seq provides a comprehensive overview of the entire transcriptome, including mRNA, non-coding RNAs, rRNA, and tRNA. This broad coverage reveals complex layers of gene regulation that other methods may overlook.
2. Accurate Gene Expression Insights
By measuring the abundance of RNA transcripts, RNA-seq accurately identifies which genes are active and to what degree. This information is invaluable for understanding developmental processes, disease mechanisms, and cellular responses.
3. Detection of Alternative Splicing
RNA-seq excels at capturing alternative splicing events, in which a single gene can produce multiple RNA transcripts. This level of detail is crucial for unraveling the complexity of gene regulation.
5. Unbiased Data
Unlike traditional methods (e.g., microarrays), RNA-seq does not rely on prior knowledge of target sequences. This unbiased approach helps avoid cross-hybridization artifacts and ensures high sensitivity for both lowly and highly expressed genes.
6. Versatile Applications
Researchers use RNA-seq across diverse fields, from basic research to cancer diagnostics, drug discovery, infectious disease research, and personalized medicine. Its versatility makes it a go-to technique in many laboratories.
7. Single-Cell Resolution
Single-cell RNA-seq (scRNA-seq) technology enables the analysis of individual cells, providing unprecedented clarity about cellular heterogeneity within tissues. This approach can reveal rare cell populations and intricate cell-to-cell interactions, as demonstrated by studies like the single-cell transcriptomics of human embryos, which identified diverse sympathoblast lineages with potential implications for neuroblastoma (Developmental Cell, 2022).
RNA-Seq Workflow
A standard RNA-seq workflow typically involves the following steps:
RNA Extraction
Isolate high-quality RNA from your sample. This step is essential for reliable downstream results.
Tip: Use established RNA isolation protocols and kits designed to minimize RNA degradation.
cDNA Library Preparation
Convert extracted RNA to cDNA via reverse transcription.
Fragment the cDNA and add adapter sequences to enable sequencing.
Key Consideration: Ensure the library prep method aligns with your specific research goals (e.g., strand-specific library prep).
MGI Integration: The MGIEasy RNA Library Preparation Kit and MGIEasy RNA Directional Library Prep Kit support strand-specific protocols, crucial for analyzing non-coding RNAs and splice variants.
Sequencing
Load the prepared cDNA library onto an NGS platform to generate short reads.
MGI Tip: The choice of platform—such as the DNBSEQ-G400 or DNBSEQ-T7—will depend on your desired throughput and read length.
Data Analysis
Align the short reads to a reference genome or assemble them de novo.
Quantify the abundance of each RNA transcript.
Perform downstream analyses like differential expression, alternative splicing, and gene fusion detection.
MGI Automation Systems
For labs seeking high-throughput or more automated workflows, MGI automation systems (e.g., MGISP-960 and MGISP-NE384) help streamline from RNA extraction to library construction. These workstations reduce manual errors, improve reproducibility, and efficiently prepare samples for sequencing on DNBSEQ™ platforms.
Applications of RNA Sequencing
RNA-seq is incredibly versatile, with applications that include: Developmental Biology: Track gene expression changes during organismal development. For instance, single-cell transcriptomics has uncovered intricate gene expression patterns during embryonic development, offering insights into developmental disorders and cellular differentiation processes (PubMed, 2022).
Cancer Research: Identify oncogenic pathways, detect tumor heterogeneity, and discover biomarkers. A single-cell and spatially resolved atlas of human breast cancers has highlighted the heterogeneity and spatial organization of tumor cells, aiding in the understanding of tumor microenvironments (Cell, 2022).
Infectious Diseases: Study pathogen-host interactions at the transcriptional level.
Drug Discovery: Assess the impact of therapeutic compounds on gene expression.
Personalized Medicine: Tailor treatments based on an individual’s unique transcriptome.
Beyond RNA-seq: Spatial Transcriptomics
MGI partners with Stomics to offer spatial omics solutions, such as Stereo-seq, which combines high-throughput RNA sequencing with spatial localization in tissue sections. Studies like the single-cell atlas of human breast cancers have demonstrated the power of spatial transcriptomics in revealing cell-to-cell interactions within complex tissues (Cell, 2022).
Conclusion
RNA sequencing has revolutionized how researchers study transcriptomes, offering an unparalleled view of gene expression and regulatory mechanisms. From single-cell RNA-seq to direct RNA sequencing, publications such as those examining human embryo development (Developmental Cell, 2022) and tumor heterogeneity (PubMed, 2022) underline the transformative potential of these technologies.Ready to Optimize Your RNA-Seq Workflow with MGI?
Learn more about DNBSEQ™ Sequencers for scalable and accurate transcriptome analysis.
Explore MGIEasy™ Kits for streamlined library prep, including rRNA depletion and directional RNA kits.
Discover MGI Automation Systems to reduce hands-on time and enhance throughput for your RNA-seq projects.
Push boundaries with Spatial Transcriptomics powered by Stereo-seq for in-depth insights into cellular architecture.
DNBSEQ-T7
DNBSEQ-T7 delivers up to 6 TB of high-quality data daily, making it ideal for deep exome, whole genome, transcriptome, and epigenome sequencing. Powered by MGI's DNBSEQ™ technology, it offers ultra-high throughput, speed, and flexibility.
