Obtain a more comprehensive set of transcript isoforms
The PacBio Isoform Sequence (Iso-Seq) method generates full-length cDNA sequences – from 5’ to the poly-A tail – to confidently characterize the full transcriptome.
The Iso-Seq method employs high-fidelity (>99% accurate) long reads to survey transcript diversity, either broadly or in a targeted fashion, revealing key information about the frequency and types of alternative transcription to improve genome annotation and gene discovery.
Single Molecule, Real-Time (SMRT) Sequencing enhances RNA sequencing, allowing you to:
- Discover novel genes and isoforms, even in well-characterized samples
- Detect alternative polyadenylation motifs
- Identify promoters and splice sites in comprehensive gene models
- Improve accuracy of RNA-seq quantification with isoform-level resolution
 | Sample & Library Preparation |
| Prepare full-length transcripts with flexible sample and library workflows |
 | Sequencing |
| Simplify sample prep workflow and reduce project costs by using the Sequel System. |
 | Data Analysis |
| Output high-quality, full-length transcript sequences with no assembly required. |
Application Brief: Learn more about these best practices for long read RNA sequencing
New to the Iso-Seq Method?
New to the Iso-Seq Method?Learn how it can help with your plant or animal project by checking out Introduction to the Iso-Seq Method: State of the Art for Full-Length Transcriptome Sequencing
Iso-Seq Project Calculator
Tell us about your plant or animal RNA sequencing project and receive an estimate on the time and materials needed using the Iso-Seq method on the Sequel System.
Spotlight: High-resolution view of transcriptional landscapes in maize and sorghum
Characterization of maize and sorghum isoforms from Iso-Seq analysis detected >40% of isoforms as novel and many alternative splicing patterns. Figure A shows the classification of isoforms of both maize and sorghum. Figure B shows the distribution of splicing patterns across tissues in both maize and sorghum.
Wang, B. et al. (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. GenomeResearch 28:1-12.
Selected Resources
- Qiao, Dahe et al. (2019) Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis). Scientific reports
- Masonbrink, Rick et al. (2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics
- Bruijnesteijn, Jesse et al. (2018) Extensive alternative splicing of KIR transcripts. Frontiers in immunology
- Chao, Yuehui et al. (2018) Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing. BMC plant biology
- Kim, Bo-Mi et al. (2018) The genome of common long-arm octopus Octopus minor. GigaScience
- Wen, Ming et al. (2018) Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing. GigaScience
- Chen, Wenbo et al. (2018) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch) BioRxiv
- Gupta, Ishaan et al. (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nature biotechnology
- Dougherty, Max L et al. (2018) Transcriptional fates of human-specific segmental duplications in brain. Genome research
- Tran, Hue T M et al. (2018) Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant biotechnology journal
- Mathew, Lolita G et al. (2018) ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-selected pink bollworm. Scientific reports
- Nyima, Tashi et al. (2018) An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley BioRxiv
- Nudelman, German et al. (2018) High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome research
- Yan, Bo et al. (2018) SMRT-Cappable-seq reveals complex operon variants in bacteria. Nature communications
- Li, Yao et al. (2018) A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing. DNA research
- Kumari, Romika et al. (2018) PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA
- Zhu, Chunhui et al. (2018) Transcriptome profiling using Illumina- and SMRT-based RNA-seq of hot pepper for in-depth understanding of genes involved in CMV infection. Gene
- Chen, Xiaojun et al. (2018) Transcriptome-referenced association study of clove shape traits in garlic. DNA Research
- Zuo, Chunman et al. (2018) Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnology for biofuels
- Wang, Bo et al. (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Research
- Kronenberg, Zev N et al. (2018) High-resolution comparative analysis of great ape genomes. Science
- Zhang, Hangxiao et al. (2018) Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. BMC plant biology
- Cantsilieris, Stuart et al. (2018) Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family. Proceedings of the National Academy of Sciences of the United States of America
- Ren, Panrong et al. (2018) Molecular mechanisms of acclimatization to phosphorus starvation and recovery underlying full-length transcriptome profiling in barley (Hordeum vulgare L.). Frontiers in plant science
- Magrini, Vincent et al. (2018) Improving eukaryotic genome annotation using single molecule mRNA sequencing. BMC genomics
- Workman, Rachael E et al. (2018) Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris GigaScience
- Filichkin, Sergei A et al. (2018) Abiotic stresses modulate landscape of poplar transcriptome via alternative splicing differential intron retention, and isoform ratio switching. Frontiers in plant science
- Tardaguila, Manuel et al. (2018) SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome research
- Makita, Yuko et al. (2018) Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. BMC genomics
- Wang, Maojun et al. (2018) A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. The New phytologist
- Gao, Shan et al. (2018) Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data. Mitochondrion
- Kuo, Richard I et al. (2017) Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC genomics
- Wang, Bo et al. (2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nature communications
- Westbrook, Catherine J et al. (2015) No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Human immunology
- Poster: Tseng, Elizabeth et al. (2019) Haplotyping using full-length transcript sequencing reveals allele-specific expression
- Poster: Vierra, Michelle et al. (2019) Library prep and bioinformatics improvements for full-length transcript sequencing on the PacBio Sequel System
- Poster: Vierra, Michelle et al. (2018) Full-length transcript profiling with the Iso-Seq method for improved genome annotations
- Poster: Vierra, Michelle et al. (2018) Characterizing the pan-genome of maize with PacBio SMRT Sequencing
- Poster: Concepion, C., et al. (2018) De novo assembly and preliminary annotation of the Schizocardium californicum genome
- Poster: Tseng, E., et al. (2018) Haplotyping of full-length transcript reads from long-read sequencing can reveal allelic imbalances in isoform expression
- Poster: Vierra, M. et al. (2017) From RNA to full-length transcripts: The PacBio Iso-Seq method for transcriptome analysis and genome annotation
- Poster: Clark, T et al. (2017) Full-length cDNA sequencing on the PacBio Sequel platform
- Badgett, Marty (2019) AGBT Presentation: The Sequel II System – the next evolution of SMRT Sequencing
- Blethrow, Justin (2019) PAG Conference: How SMRT Sequencing is accelerating plant and animal genomics
- Tseng, Elizabeth (2019) PAG Conference: Iso-Seq analysis for plant & animal genomes – annotation evaluation & phasing
- Korlach, Jonas and Corney, Dave (2018) Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads
- (2018) Tutorial: Iso-Seq analysis application [SMRT Link v6.0.0]
- Pillai, Nisha (2018) Webinar: Survey of transcriptome diversity using Iso-Seq analysis
- Korlach, Jonas (2017) PAG PacBio Workshop: SMRT Sequencing for complete genomes
- Kuo, Richard (2017) PAG PacBio Workshop: Using the Iso-Seq method to fill in your a_no__tion
- PacBio Certified Service Providers (2018)
- Application Brief: Long-read RNA sequencing – Best Practices (2018)
- SMRT Sequencing Brochure: Revolutionize genomics with SMRT Sequencing (2018)
- Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center (2017)
- Case Study: First comprehensive view of maize genome reveals regulatory and structural mechanisms (2016)