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.
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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 Systems. |
 | 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
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
- Ye, Jiabao et al. (2019) A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis Industrial Crops and Products
- Tørresen, Ole K et al. (2019) Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic acids research
- He, Yaoxi et al. (2019) Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nature communications
- Liu, Qin et al. (2019) A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. GigaScience
- Watson, Corey T et al. (2019) A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains. Immunology and cell biology
- Low, Wai Yee et al. (2019) Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation BioRxiv
- Yang, Zhaoen et al. (2019) Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature communications
- Wan, Ying et al. (2019) Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. BMC genomics
- Warr, Amanda et al. (2019) An improved pig reference genome sequence to enable pig genetics and genomics research BioRxiv
- Wang, Bo et al. (2019) Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize BioRxiv
- Zhuang, Weijian et al. (2019) The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature genetics
- Zhang, Xiujuan et al. (2019) Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Fish & shellfish immunology
- Chen, Wenbo et al. (2019) Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). GigaScience
- Minio, Andrea et al. (2019) Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3
- 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
- Deiss, Thaddeus C et al. (2019) Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cellular & molecular immunology
- 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
- 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
- Nudelman, German et al. (2018) High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome research
- Zeng, Xingquan et al. (2018) Improved high-quality genome assembly and annotation of Tibetan hulless barley BioRxiv
- 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
- Shen, Yanting et al. (2018) De novo assembly of a Chinese soybean genome. Science China. Life sciences
- Pollard, Martin O et al. (2018) Long reads: their purpose and place. Human molecular genetics
- 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
- Poster: Tseng, Elizabeth et al. (2020) A complete solution for high-quality genome annotation using the PacBio Iso-Seq method
- 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
- Kuo, Richard (2020) Customer Experience: A new view of non-coding RNA with PacBio HiFi reads
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Conesa, Ana (2020) Customer Experience: Improving transcriptome research with PacBio HiFi reads
- Mars, Kristin and Laird Smith, Melissa and Vinnere Pettersson, Olga and Hardigan, Michael (2020) Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Kronenberg, Zev (2020) PAG Conference: Characterizing genetic differences between great apes using Iso-Seq data
- Vierra, Michelle (2020) PAG Conference: PacBio update on products and HiFi applications
- Korlach, Jonas (2020) PAG Conference: Workshop introduction
- Sheynkman, Gloria, and Tseng, Elizabeth (2019) Webinar: Discover full-length RNA sequencing – No assembly required
- Cegarra, Ana Conesa (2019) User Group Meeting: From long reads to transcript function: Bioinformatics tools for Iso-transcriptomics analysis
- Wheeler, Nic (2019) User Group Meeting: Long-read RNA Sequencing in neglected human parasites
- Mars, Kristin (2019) User Group Meeting: No Assembly Required – Making the most of Iso-Seq data
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- Trojahn, Shawn (2019) User Group Meeting: Using grizzly bears to unlock the biomedical promise of hibernation
- Kingan, Sarah and McKernan, Kevin (2019) Webinar: Smoking out structural variants in the cannabis genome
- 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
- Kuo, Richard (2018) Webinar: Using Iso-Seq analysis to build a better annotation
- Williams, John (2018) PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through 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
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Application Brochure: What can you do with one SMRT Cell? (2020)
- PacBio Certified Service Providers (2020)
- Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing (2019)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2019)
- Application Brief: Long-read RNA sequencing – Best Practices (2019)
- 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)