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Thursday, March 30, 2017

At AACR, Revealing Structural Variants and a New SMRT Grant Program

We’re excited to be heading to Washington, DC, for the annual meeting of the American Association for Cancer Research. The PacBio team always enjoys hearing about the latest in cancer translational research at AACR, along with thousands of leading scientists in the field. Many of those scientists have already learned that SMRT Sequencing provides a unique view into cancer, revealing structural variation, phasing distant variants, and delivering full-length isoform sequences. With uniform coverage, industry-leading consensus accuracy, and reads extending to tens of kilobases, PacBio long-read sequencing gives researchers the ability to monitor and make sense of even the most complex…

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Wednesday, August 12, 2015

Using SMRT Sequencing, Scientists Uncover Unexpected Transcript Diversity in Fungi

A new PLoS One publication from scientists at the Joint Genome Institute, University of Minnesota, and other organizations demonstrates that fungal genomes may contain far more transcript diversity than previously thought. In “Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing,” lead author Sean Gordon, senior author Zhong Wang, and collaborators used long-read isoform sequencing to characterize four fungal species. In addition to widespread alternative splicing, they found evidence of polycistronic transcription units that could be important engineering targets for genetic manipulation of fungi. The scientists turned to SMRT® Sequencing to escape the limitations of short-read transcriptome sequencing. “The…

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Thursday, June 11, 2015

Updated! Data Release: Human MCF-7 Transcriptome

UPDATE: Our R&D team has added a new dataset for the MCF-7 human breast cancer transcriptome, originally released in 2013. The new results were produced using 28 SMRT® Cells with 4-hour movies and P5-C3 chemistry. Sizing was performed with the SageELF™ platform (fractions collected: 1-2 kb, 2-3 kb, 3-5 kb, and 5-10 kb). Sequencing of the larger fractions with our newer sequencing chemistry that generates longer reads added longer transcripts (up to 10 kb) to the MCF-7 dataset, which previously had only transcripts up to 4 kb. New FASTA and GFF files are available, representing the new combined dataset. Raw…

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Tuesday, June 9, 2015

Attend Our Worldwide User Meetings & SMRT Informatics Developers Conference

If you’d like to hear about the latest applications of SMRT® Sequencing from users, we have several events coming up. Our worldwide user group meetings and workshops feature PacBio users sharing their latest research, tips, and protocols, as well as our staff providing training and updates on products and methods to optimize your research. We’re always humbled by the quality and variety of science presented at these meetings. And for the bioinformatics crowd, we have a new event in August focused on developing new analytical tools for PacBio® data. Here’s more detail on each event, including registration details: Americas East…

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Wednesday, May 6, 2015

Tutorial on the Iso-Seq Method: Applications, Protocol, and Experimental Design

If you missed our recent webinar on isoform sequencing with the PacBio® platform, we’ve made the full recording available for on-demand access. “Iso-Seq™ Method: Sample Prep and Experimental Design for Full-Length cDNA Sequencing” offers an overview of the application, along with specific sample prep tips, factors to consider when designing an experiment, and suggestions about what kinds of projects can take advantage of this method. Hosted by our own Tyson Clark, the webinar begins with a look at why it’s important to capture full-length transcripts. There are known human genes that have very different functions depending on which splice variant…

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Thursday, March 26, 2015

In Chronic Myeloid Leukemia Study, SMRT Sequencing Detects Resistance Mutations Early, New Splice Isoforms and More

Scientists from Uppsala University report in a recent paper that using the Iso-Seq™ method with SMRT® Sequencing allowed them to detect and monitor mutations in the BCR-ABL1 fusion gene for patients with chronic myeloid leukemia (CML). Screening mutations in this region is important for determining the point at which these patients become resistant to tyrosine kinase inhibitor (TKI) therapies, and is currently performed in the clinic using Sanger sequencing, quantitative RT-PCR, and other assays. The paper, “Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing,” was published last month in BMC Cancer from lead author Lucia…

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Wednesday, February 4, 2015

High-Quality Genome Assembly and Transcriptome of Cotton Using SMRT Sequencing

A recent research partnership with KeyGene, a Dutch plant genomics and crop improvement company, has resulted in an integrated whole-genome assembly and transcriptome of Gossypium hirsutum, or tetraploid cotton. This is the first known complete assembly for a polyploid crop with a genome larger than 2 Gb. KeyGene has a long established reputation for generating high-quality data even for very complex genomes. For this project, the cotton genome was sequenced with 38x coverage using Single-Molecule, Real-Time (SMRT®) Sequencing. Assembly of PacBio® long reads reduced the number of contigs from more than 1 million in an existing short-read assembly to fewer…

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Thursday, January 29, 2015

Register Now: Isoform Sequencing Webinars Offer Tips on Method and Analysis

If full-length transcript information would be useful for your research, please join us for two upcoming webinars. Our scientists will offer tips for how to optimize the Iso-Seq™ method with the PacBio® System to meet your research goals. Our first webinar, Iso-Seq™ Method: Sample Prep and Experimental Design for Full-Length cDNA Sequencing,” will be presented by Tyson Clark, PacBio’s senior manager for next-generation applications and technologies. The talk will cover recent Iso-Seq template preparation protocol updates for creating full-length cDNAs, why full-length transcript sequence matters, and experimental design considerations. Sign up now at your preferred time: the webinar will take…

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Friday, January 23, 2015

Breaking New Frontiers in Grass Genomics to Understand Drought Tolerance with the 2014 SMRT Grant Program Winner: Oropetium thomaeum

Emerging from a myriad of interesting genome nominations, from the American cranberry to South American prawns and African Guava, Oropetium thomaeum submitted by Todd Mockler at the Donald Danforth Plant Science Center was selected as the first winner of the “Most Interesting Genome in the World” SMRT® grant program in 2014.  Also affectionately known as Oro, this grass species can be  revived with water after a long drought exposure. At 250 Mb, the genome is also the smallest amongst grasses due to compaction of complex repeat and gene structures, including previously identified expansions in osmoprotectant biosynthesis pathways. Kicking off the…

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Tuesday, January 20, 2015

Looking Ahead: The 2015 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer All of us at Pacific Biosciences are very proud of the momentum SMRT® Sequencing achieved in 2014, especially due to the more than 500 customer publications now in the literature describing its many applications. We remain deeply thankful to all the scientists who have applied our technology to gain new insights into genomes, transcriptomes, and epigenomes. By applying SMRT Sequencing to a wide variety of applications, our customers are demonstrating that long, unbiased reads have brought about new quality standards for many fields of genomic research. This exciting level of scientific activity and collaboration…

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Thursday, December 11, 2014

Review Article: Long-Read Sequencing Offers Better Understanding of Pluripotency

A new review article offers a nice overview of attempts to characterize the transcriptome of human stem cells using RNA-seq, the Iso-Seq™ method, and more. Kin Fai Au and Vittorio Sebastiano, scientists at the University of Iowa and Stanford University, respectively, contributed the review to Current Opinion in Genetics & Development. “The introduction of the RNA-Seq technology based on [second-generation sequencing technology] has provided a remarkable step forward providing a fast and inexpensive way to determine the transcriptome of a given cell type and several remarkable works have been done using this type of approach,” Au and Sebastiano write. “Nonetheless…

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Wednesday, November 12, 2014

New Transcript Study Offers Clues to Pathogenesis of Repeat Disorders Linked to FMR1

It’s been nearly two years since a team of scientists from the University of California, Davis, School of Medicine published the first-ever complete sequence of FMR1, the gene associated with a repeat expansion that causes Fragile X syndrome. That team is once again breaking new ground, this time characterizing alternative splicing and full-length transcripts of FMR1. For both studies, the scientists relied on Single Molecule, Real-Time (SMRT®) Sequencing because its uniquely long reads allowed them to span the gene and generate sequence and isoform data that would not have been possible any other way. The new paper, “Differential increases of…

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Wednesday, October 29, 2014

‘Revolutionizing HLA Typing’: Uppsala’s Ulf Gyllensten on How Long Reads Give Access to New Areas of the Human Genome

In a recent interview with Theral Timpson — part of Mendelspod’s series on long-read sequencing — Ulf Gyllensten, a scientist at Uppsala University, spoke about using PacBio® technology for HLA typing, human genome studies, transcriptomics, and more. Based in the medical genetics and genomics department, Gyllensten focuses on two areas: using systems biology to study biological variation in human physiology and studying the epidemiology of human papilloma virus and its genetic link to cervical cancer. He also works with the National Genomics Infrastructure, a national core facility in Sweden for genotyping and DNA sequencing, where he has access to all…

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Tuesday, October 21, 2014

Data Release: Whole Human Transcriptome from Brain, Heart, and Liver

In higher eukaryotic organisms, like humans, RNA transcripts from the vast majority of genes are alternatively spliced. Alternative splicing dramatically increases the protein-coding potential of eukaryotic genomes and its regulation is often specific to a given tissue or developmental stage. Using our updated Iso-Seq™ sample preparation protocol, we have generated a dataset containing the full-length whole transcriptome from three diverse human tissues (brain, heart, and liver). The updated version of the Iso-Seq method incorporates the use of a new PCR polymerase that improves the representation of larger transcripts, enabling sequencing of cDNAs of nearly 10 kb in length. The inclusion…

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Thursday, October 9, 2014

New Brain Study Reveals Higher Molecular Diversity from Alternative Splicing

A new paper from scientists in Switzerland and the US adds to recent findings about diversity of neuronal transcripts in the mammalian brain. The authors report that this study was only possible using long reads from Single Molecule, Real-Time (SMRT®) Sequencing. “Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins,” from lead author Dietmar Schreiner, senior author Peter Scheiffele, and collaborators, was published this month in the journal Neuron. The researchers are from the University of Basel, ETH Zurich, and North Carolina State University. This is the second study on neurexin mRNA diversity using PacBio® sequencing. The team tackled…

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