Video Gallery

In this webinar we present Single Molecule, Real-Time (SMRT) Sequencing and the Iso-Seq method, which allow you to generate full-length cDNA sequences — no assembly required — to characterize transcript isoforms within targeted genes or across an entire transcriptome. The presenters share how the Iso-Seq method: (1) Provides high quality, full-length transcript sequences of up to 15 kb; (2) Allows for one-day library prep on a single SMRT Cell 8M to comprehensively characterize a whole transcriptome; (3) Facilitates discovery of alternative splicing events, fusion gene detection, and allelic specific isoform detection; and (4) Enables discovery of potential cancer-specific isoforms in breast and melanoma samples.

Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is a powerful tool for phytobiome research.

In this presentation, Naomichi Matsumoto from Yokohama City University speaks about the use of SMRT Sequencing to solve Mendelian diseases, including the story of how his lab discovered a 12.4 kb structural variant that’s responsible for progressive myoclonic epilepsy in two siblings. He also reports progress in understanding repeat expansion disorders by pairing SMRT Sequencing with new analysis tools designed to highlight repetitive areas.

In this presentation, Shawn Levy from the HudsonAlpha Institute for Biotechnology and HudsonAlpha Discovery offers a look at his team’s early access experience with the Sequel II System. Recent work includes a project designed to improve sequencing results from FFPE samples with long-read data. The protocol is still being optimized, but preliminary results indicate that SMRT Sequencing improves the quality of data that can be produced from these highly degraded samples. Looking ahead, Levy’s team will be using SMRT Sequencing to generate about 7,000 long-read genome assemblies for the All of Us program.

In this presentation, Emily Hatas of PacBio offers a look a how SMRT Sequencing has changed over the years as well as the most common applications in human genome analysis: high-throughput structural variant detection; comprehensive variant detection; and de novo assembly of reference genomes.

In this PacBio User Group Meeting presentation, Ana Conesa Cegarra from the University of Florida spoke about Iso-Seq analysis tools developed by her group, which created the popular SQANTI tools for Iso-Seq data QC. They’re also working on IsoAnnot to perform functional annotation at isoform resolution; validation has already been done on various species. Currently it’s a set of scripts, but her team is working to produce a more user-friendly version. Finally, tappAS is for functional diversity analysis and for prioritizing genes for validation.

In this PacBio User Group Meeting presentation, Erin Bernberg from the University of Delaware reports on using the Agilent Femto Pulse System for high-resolution, highly sensitive fragment analysis and on the low DNA input protocol, which her team used for a recent study of ice worms.

In this PacBio User Group Meeting presentation, Eugenio Daviso from Covaris talks about the use of adaptive focused acoustics for gentle cell lysis and extraction of high molecular weight DNA.

In this PacBio User Group Meeting presentation, Mitchell Vollger of the University of Washington used HiFi reads from SMRT Sequencing to study segmental duplications in the human genome. The technique significantly reduced the complexity of accurately mapping these nearly identical sequences throughout the genome; it also reduced the amount of compute power needed compared to a previous PacBio assembly using continuous long reads instead of circular consensus sequencing. Despite generating less data with the HiFi assembly, the team still resolved 30% more segmental duplications with the new approach.

In this PacBio User Group Meeting presentation, Nic Wheeler of University of Wisconsin-Madison, speaks about RNA sequencing for filarial nematodes associated with understudied tropical diseases. His team used Iso-Seq analysis to improve gene models and achieve better transcriptome coverage for these worms, which typically have poorly annotated and fragmented genome assemblies. While getting enough RNA to study is a technical challenge, the group still managed to generate full-length isoforms, many of which were novel or contained novel junctions.

To start Day 2 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on lowering DNA input amounts for SMRT Sequencing workflows. Updates include a more robust shearing method, a revised AMPure size selection, and introduction of multiplexing low input samples. Finally, the use of HiFi sequencing with low input results in a more complete genome assembly. Jonas closes by mentioning that the low DNA input protocol is now available and further advancements to lower input requirements even more will open opportunities for different samples, such as cancer needle biopsies.

In this PacBio User Group Meeting lightning talk, Masako Nakanishi presents a study of how the gut microbiome alters an organism’s susceptibility to colonic ulceration; next, she plans to examine cause and effect by evaluating results of fecal transplants in mice.

In this PacBio User Group Meeting lightning talk, Alexandra Pike of MIT presents a study of TIN2, a telomere-binding protein, which is mutated in some short telomere syndromes. By pairing the Iso-Seq method with CRISPR, her team revealed a previously uncharacterized TIN2 isoform that may have a functional difference for individuals with these syndromes.

In this PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. By using SMRT Sequencing, his team generated higher-resolution data about viral genomes and aims to use this information as a guide to how these genomes function.

In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.