Sample Submission Guidelines
Why Full Length LncRNA Sequencing Matters
Long non-coding RNAs (lncRNAs) are >200 nt transcripts that regulate gene expression, development, epigenetics, and disease pathways. Their functions are often cell-type-specific and highly dependent on alternative splicing. However, short-read sequencing fragments RNA into small pieces, making it difficult to reconstruct complete isoforms or quantify them accurately.
Nanopore Full Length LncRNA Sequencing solves this problem by generating reads that span the entire transcript from 5' to 3'. This enables researchers to identify novel lncRNAs, resolve splice junctions, and quantify isoforms directly—providing a more complete view of the transcriptome.
Our Nanopore Full Length LncRNA Sequencing Solution
CD Genomics' platform integrates advanced Oxford Nanopore long-read technology with optimized RNA library preparation to deliver accurate, isoform-level insights into the lncRNA transcriptome.
Technical Parameters
- Input: Total RNA (≥2 µg, RIN ≥7, rRNA-depleted)
- Read length: up to 10–20 kb continuous single-molecule reads
- Coverage: single-transcript 5' to 3' sequencing without fragmentation
- Throughput: millions of reads per run, scalable for large transcriptomes
- Data outputs: FASTQ, BAM/GTF alignment, isoform annotations, quantification matrices
Technical Advantages
- Complete transcript coverage – direct sequencing of entire lncRNAs, eliminating the need for assembly
- Splicing resolution – reliable identification of exon skipping, intron retention, and complex splice variants
- Isoform-level quantification – more accurate measurement of expression compared with short-read approaches
- Broad RNA detection – capture of lncRNA, mRNA, tRNA, and small RNA within the same dataset
- Poly(A)-independent detection – enables discovery of non-polyadenylated lncRNAs often missed by conventional methods
Problems Solved for Researchers
- Overcomes short-read limitations – avoids incomplete isoform reconstruction caused by fragmented sequencing
- Improves accuracy in biomarker discovery – detects rare or novel lncRNAs relevant to disease and development
- Supports mechanistic insights – clarifies how isoforms and splicing events regulate biological processes
- Expands transcriptome annotation – identifies uncharacterized transcripts to enrich genomic databases
Short-Read vs. Full-Length LncRNA Library Construction
A clear comparison of short-read RNA-seq and Nanopore full-length lncRNA sequencing highlights why long-read technology delivers more reliable transcriptome insights.
| Feature | Short-Read LncRNA Library Construction | Nanopore Full-Length LncRNA Library Construction |
|---|---|---|
| RNA Processing | Total RNA → rRNA removal or poly(A) enrichment → RNA fragmentation | Total RNA → rRNA removal → RNA integrity preserved, no fragmentation |
| Library Preparation | Random priming, cDNA synthesis, multiple PCR cycles, adapter ligation | Full-length cDNA synthesis, minimal amplification, adapter ligation for Nanopore |
| Read Length & Coverage | 50–300 bp fragments; requires computational assembly | 10–20 kb continuous reads spanning transcripts from 5' to 3' |
| Isoform & Splicing Detection | Predicted by assembly; many events remain unresolved | Direct detection of true splice junctions, exon skipping, and isoform diversity |
| Quantification Accuracy | Fragment counts prone to bias, especially for long or low-abundance transcripts | Isoform-level quantification with consistent, reproducible expression profiles |
| Novel Transcript Discovery | Limited to known annotations and poly(A)+ lncRNAs | Detects unannotated and non-poly(A) lncRNAs with broad RNA coverage |
| Bias & Error Sources | Fragmentation and PCR introduce assembly errors, 3'/5' bias | Higher raw error rate, but reduced assembly bias; corrected via bioinformatics |
| Typical Applications | Differential gene expression, known gene studies | Isoform discovery, splicing analysis, biomarker identification, novel lncRNA annotation |
Why This Comparison Matters
Traditional short-read sequencing is powerful for gene-level expression studies but struggles with isoform reconstruction and alternative splicing detection. In contrast, Nanopore full-length lncRNA sequencing provides continuous read coverage across entire transcripts, enabling accurate isoform quantification, novel lncRNA discovery, and mechanistic insights into transcriptome regulation.
Applications in Research
Nanopore Full Length LncRNA Sequencing supports a wide range of biological and biomedical studies:
Developmental Biology – build lncRNA atlases across tissues, species, and stages of differentiation
Oncology – uncover isoform-level biomarkers and splicing regulation in cancer progression
Neuroscience & Immunology – analyze lncRNA regulation in immune response and neural processes
Environmental Toxicology – track lncRNA expression changes under chemical or pollutant exposure
Evolutionary Biology – identify conserved motifs, sORFs, and miRNA-binding sites in novel lncRNAs
Service Workflow
From consultation to results, CD Genomics delivers a complete solution:
Project consultation – design tailored to your research goals
Sample QC – rRNA depletion and RNA quality control
Library preparation – full-length cDNA synthesis and adapter ligation
Nanopore sequencing – long-read coverage of lncRNA isoforms
Bioinformatics – isoform annotation, quantification, functional insights
Data delivery – raw data, processed files, annotated reports
Why Partner with CD Genomics
- Over a decade of expertise in next-generation and long-read sequencing
- Proven track record with Oxford Nanopore technologies
- Dedicated bioinformatics team specializing in transcriptome analysis
- Flexible, research-use-only solutions for academia, biotech, and pharma
- Reliable data quality, CRO-grade standards, and secure data delivery
Deliverables
You will receive:
- Raw data files (FASTQ)
- Processed alignment files (BAM/GTF)
- Isoform annotation and expression quantification tables
- Comprehensive analysis report (PDF + Excel)
- Visualizations of isoform structures and splicing events
Sample Requirements
Total RNA: ≥ 2 µg, RIN ≥7, OD260/280 = 1.8–2.0
Accepted sample types: tissues, cultured cells, blood-derived RNA, FFPE upon consultation
Shipping: Send samples on dry ice for RNA integrity preservation
Frequently Asked Questions (FAQ)
Q1. Why choose full-length Nanopore sequencing instead of Illumina short-read RNA-seq?
Nanopore captures complete isoforms and resolves splicing events, avoiding assembly artifacts from fragmented reads.
Q2. Can non-poly(A) lncRNAs be detected?
Yes. Our protocol does not rely on poly(A) enrichment, allowing for broader transcript coverage.
Q3. What sequencing depth is recommended?
We recommend 10–20 million reads for standard transcriptome profiling, with higher depth for low-abundance lncRNAs.
Q4. Do you provide bioinformatics support?
Yes. We deliver isoform-level analysis, quantification, functional annotation, and custom pipelines tailored to your study.
Q5. What other Nanopore services do you provide?
We also offer Nanopore Target Sequencing and multi-transcript profiling options.
Integrated Demo Results of Nanopore Full Length LncRNA Sequencing
Frequently Asked Questions
What is "full-length lncRNA sequencing" and how does it differ from standard RNA-seq?
Full-length lncRNA sequencing refers to sequencing strategies (typically via long-read technologies) designed to capture transcripts from the 5' end through splice junctions to the 3' end, so you get the full isoform without relying heavily on assembly of short fragments. Standard (short-read) RNA-seq often requires breaking RNA into pieces, assembles reads computationally, which can miss splice variants, exon boundaries, transcription start or end, and low-abundance transcripts. Full-length sequencing improves detection of novel isoforms, accurate splice-junction mapping, and quantification of complete transcripts.
Do you need special sample quality for Nanopore full-length lncRNA sequencing?
Yes, sample quality has a strong impact: total RNA must be of high integrity (low degradation), with good purity (low protein, phenol, or salt contamination), and efficient removal of rRNA. Because full-length reads are more sensitive to RNA breaks, starting with intact RNA improves yield of full transcripts. Low-abundance and long transcripts are especially vulnerable to degradation.
Can we detect novel lncRNAs or splice variants that are not in the reference annotation?
Absolutely. One of the major strengths of full-length lncRNA sequencing is its ability to uncover unannotated transcripts, previously unrecognized splice junctions, and novel isoforms. Because reads cover exon structure completely (including alternative splice sites), you can identify variants that short-read methods often miss.
How accurate is expression quantification with full-length lncRNA sequencing compared to short-read?
Expression quantification is more reliable at the isoform level when you have full-length reads, because you minimize bias from assembly, fragment length, and fragmentation. While base-level error rates may be somewhat higher in long-read technologies, downstream correction and alignment tools allow very good quantification, especially for moderate to high expression transcripts.
Which RNA types can be captured in this sequencing? Does it have to be poly(A)-tailed lncRNAs?
You can capture a broad spectrum: poly(A) lncRNAs, non-poly(A) lncRNAs, mRNAs, and other long non-coding transcripts depending on library prep protocol (e.g. rRNA depletion instead of poly(A) enrichment). Non-poly(A) lncRNAs often require rRNA removal + custom priming or adaptor ligation methods.
What are typical read lengths and output quality for this service?
Typical full-length reads span entire transcript lengths (several kb long), depending on transcript length and quality of input RNA. Quality includes consistent splice junction detection, coverage from 5' to 3' ends, low fragmentation bias. Output includes raw reads, aligned isoforms, and reproducible expression estimates.
Is this type of sequencing suitable for discovering novel biomarkers or in translational / clinical research?
Yes. Because full-length lncRNA sequencing resolves entire isoform structure and enables detection of previously unannotated transcripts or splice variants, it is highly valuable for biomarker discovery, disease mechanism studies, and translational research. With proper sample handling, validation, and bioinformatics pipelines, results can support downstream assays or diagnostic marker validation.
Case Study: Nanopore Full-Length lncRNA Sequencing Reveals lncRNA-Mediated Regulation of Fruit Coloration
Reference: Yu J, Qiu K, Sun W, et al. A long noncoding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis. Plant Physiology. 2022;189:66–83. https://doi.org/10.1093/plphys/kiac049
1. Background
Anthocyanin pigments determine the red coloration of apple peels, directly influencing fruit quality and consumer preference. While light and ethylene are known regulators, the molecular mechanisms linking these signals remained unclear. The study investigated whether long noncoding RNAs (lncRNAs) contribute to the regulation of anthocyanin biosynthesis during high-light exposure in apple (Malus domestica).
2. Methods
Transcriptome sequencing of apple peels exposed to different light conditions was performed to identify light-responsive lncRNAs.
Weighted gene co-expression network analysis (WGCNA) identified MdLNC610 as highly correlated with anthocyanin and ethylene production.
Functional validation included:
- RT-qPCR expression analysis under light and inhibitor treatments.
- Overexpression and silencing of MdLNC610 and MdACO1 in apple fruit and calli using Agrobacterium-mediated transformation.
- Hi-C chromatin conformation capture to assess physical proximity between MdLNC610 and MdACO1.
3. Results
High-light treatment significantly increased both anthocyanin accumulation and ethylene production in apple fruit.
MdLNC610 expression was induced by high light and positively correlated with MdACO1, a key ethylene biosynthesis gene.
Overexpression of MdLNC610 led to higher ethylene levels and enhanced red coloration, while silencing suppressed pigmentation.
Hi-C data confirmed physical association between MdLNC610 and MdACO1, suggesting a cis- or trans-regulatory mechanism.
Functional validation of lncRNA MdLNC610: Overexpression promotes ethylene production and anthocyanin accumulation, while silencing suppresses coloration in apple fruit under high-light conditions.
4. Conclusions
This case demonstrates that Nanopore full-length lncRNA sequencing and integrative transcriptomics can identify novel regulatory lncRNAs like MdLNC610, which mediate key physiological traits such as apple peel coloration. By capturing complete isoforms and resolving expression patterns, long-read sequencing provides critical insights into noncoding RNA–mRNA regulatory networks.
References:
- Kyle Palos, et al. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. Plant Cell, 2022.
- Li N, et al. A novel trans-acting lncRNA of ACTG1 that induces the remodeling of ovarian follicles. International Journal of Biological Macromolecules. 2023
- Yu J, Qiu K, Sun W, et al. A long non-coding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis. Plant Physiology, 2022.
- Lan Z, et al. The interaction between lncrna snhg6 and hnrnpa1 contributes to the growth of colorectal cancer by enhancing aerobic glycolysis through the regulation of alternative splicing of PKM. Frontiers in Oncology, 2020.
- Cao M X,et al. Identification of potential long noncoding RNA biomarker of mercury compounds in zebrafish embryos. Chemical Research in Toxicology, 2019.
