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Monday, March 31, 2014

New Software Release: SMRT Analysis Upgrade for Iso-Seq Analysis and HLA Allele Phasing

Today we announced the release of a software upgrade for our Single Molecule, Real-Time (SMRT®) DNA Sequencing platform. SMRT Analysis 2.2 provides enhanced functionality to support two additional applications that uniquely benefit from our long-read sequencing technology: Iso-Seq™ full-length transcript /isoform sequencing, and human leukocyte antigen (HLA) allele phasing. The study of mRNA transcript isoforms has been challenging due to the short read lengths of other sequencing technologies. Since Iso-Seq analysis allows for the capture of full-length transcripts, scientists can use this approach to identify alternatively spliced forms of a gene, detect novel genes and isoforms, or perform transcriptome-wide analysis…

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Monday, March 31, 2014

This Week: Sample Prep Webinar on 10 Kb Template Prep

If you love long reads, you won’t want to miss this week’s webinar on sample prep for Single Molecule, Real-Time (SMRT®) Sequencing. We will focus on automation solutions for 10 Kb template preparation, including new high-throughput sample prep kits, compatible automated liquid handling platforms, and sample data. Register now for the webinar, with your choice of times: Tuesday, April 1 5:00 p.m. PDTWednesday, April 2 8:00 a.m. PDT Our presenters will be PacBio scientists Kristi Spittle Kim and Michael Weiand. Kristi, an applications scientist in our technical support group, has been working in the genomics field since 2006. At PacBio,…

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Thursday, March 27, 2014

As Genome Editing Gains Traction, SMRT Sequencing Provides Accurate View of Results

A new paper published in Cell Reports describes how Single Molecule, Real-Time (SMRT®) Sequencing can be used to greatly improve outcome reporting for a variety of popular genome-editing approaches. “Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing” comes from lead authors Ayal Hendel and Eric Kildebeck from the Porteus lab at Stanford University, along with other collaborators at Stanford and the Georgia Institute of Technology. The goal for this study was to contribute to the tremendous innovations occurring in the genome editing field — from CRISPR to TALENs and more — by finding a better tool to measure results…

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Wednesday, March 26, 2014

Importance of Finished Microbial Genome Highlighted for Ethanol-Generating Clostridium

A paper in BioMed Central’s Biotechnology for Biofuels journal demonstrates how finished microbial genomes using Single Molecule, Real-Time (SMRT®) Sequencing are having an impact on the biotechnology industry. The publication, “Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia,” comes from scientists at Oak Ridge National Laboratory, the University of Tennessee, and New Zealand-based biofuels company LanzaTech. Lead authors Steven Brown and Shilpa Nagaraju and their colleagues used PacBio® sequencing to generate a finished genome sequence for a complex class III microbe that previously could not…

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Friday, March 21, 2014

ABRF Preview: Off to the Land of Core Labs and Hot Air Balloons

Members of the PacBio team will be heading down to Albuquerque this weekend for the annual conference of the Association of Biomolecular Resource Facilities (ABRF). It’s a big year for the association, which is celebrating its 25th anniversary, and we’re looking forward to participating. ABRF is a meeting where we connect with the most innovative leaders of the core facility community. As PacBio blog readers know, core labs are very important in the SMRT® Sequencing landscape. Last year we launched our directory of service providers that offer sequencing with the PacBio® platform, and many scientists have told us how useful…

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Wednesday, March 19, 2014

Assessment of Highly Complex Alternative Splicing of Neurexins Performed with SMRT Sequencing

A new paper in the Proceedings of the National Academy of Sciences from the laboratories of Stephen R. Quake and Thomas C. Südhof (both at Stanford University) describes the direct, full-length transcript sequencing of RNA molecules that are essential to synapse formation in the mammalian brain. The team used Single Molecule, Real-Time (SMRT®) Sequencing to analyze full-length mRNAs from different members of the neurexin gene family and used that information to examine alternative splicing events. In the publication entitled “Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing,” the scientists highlight the importance of understanding alternative splicing in…

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Friday, March 14, 2014

AGBT 2014 Presentation Videos: SMRT Sequencing at CSHL, Uppsala U., and Baylor College of Medicine

There were several excellent talks showcasing SMRT® Sequencing data at the annual Advances in Genome Biology and Technology conference. If you didn’t have the opportunity to see them in person, you can watch the recordings: From Cold Spring Harbor Laboratory, Dick McCombie described the need for de novo sequencing, which preserves structural information that can be missed with resequencing. Organisms presented include yeast, Arabidopsis, and rice. McCombie notes that in many cases, full chromosomes are assembled into single contigs with long-read sequencing. He also presented the longest read seen at AGBT: more than 54 Kb. Watch video: A near perfect…

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Monday, March 3, 2014

In Acinetobacter Study, Long Reads Aid in Defining Genomic Structure

A paper recently published in mBio, an open access journal from the American Society for Microbiology, reports on the sequencing and phylogenetic analysis of several drug-resistant strains of a pathogen found in hospitals. According to the authors, incorporating PacBio® sequence was critical for generating extremely long contigs for assembly and for accurately identifying chromosomal position and structure of genomic features associated with drug resistance. The publication, entitled “New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis,” from scientists at the J. Craig Venter Institute, as well as Case Western Reserve University and its…

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