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Tuesday, September 25, 2018

Iso-Seq SMRT Grant Winner to Study Alternative Splicing in Neurons

Xiaochang Zhang, an assistant professor at the University of Chicago, is poised to get a powerful new data set to help his team understand the role of alternative splicing in brain development. His project, entitled “Uncovering mRNA splicing diversity in cerebral cortex development,” was selected as the winner of the 2018 Iso-Seq SMRT Grant Program. Sequencing for this project will be carried out by our Certified Service Provider RTL Genomics. We caught up with Xiaochang to learn more about his research and how SMRT Sequencing data will make a difference. Q: What’s your research focus? A: We are interested in…

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Tuesday, September 18, 2018

Must-Have PacBio Applications & Services: Getting the Most from SMRT Sequencing

In addition to the most common applications, like whole genome sequencing for de novo assembly, there are several other features you can utilize to advance your science or incorporate to offer your customers a broad range of the best PacBio services. Here’s a sampling of the most recent updates and releases.   Iso-Seq Analysis for Genome Annotation or Targeted Isoform Discovery The isoform sequence (Iso-Seq) application generates full-length cDNA sequences – from the 5’ end of transcripts to the poly-A tail – eliminating the need for transcriptome reconstruction using isoform-inference algorithms. It’s even easier to help your customers annotate their…

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Thursday, September 13, 2018

Building a Digital Genome Ark: Vertebrate Genome Project Releases 15 New Reference Genomes

The duck-billed platypus genome is one of 15 high-quality assemblies released by the Vertebrate Genome Project When creating a global genomic ark of creatures great and small, scientists are turning to the comprehensive coverage and quality of PacBio sequencing. The Vertebrate Genomes Project (VGP), an international consortium of more than 150 scientists from 50 academic, industry and government institutions in 12 countries, recently released the first 15 of an anticipated 66,000 high-quality reference genomes representing all vertebrate species on Earth. The VGP consortium spent three years selecting technologies and workflows to produce higher quality, “platinum-level” genomes, and SMRT Sequencing was…

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Wednesday, September 12, 2018

How to Incorporate New Features into Your Sequencing Services Menu

Pacific Biosciences HQ Many people who run a sequencing core lab would prefer to focus on science instead of business, but all core lab managers know that it’s imperative to keep a steady stream of clients and projects filling the pipeline. In a recent blog post we offered 5 ways to attract more customers to your sequencing services. Now let’s take a look at how you can incorporate new services and upgrades into your facility. Keeping up with the latest and greatest advancements in sequencing technology isn’t just about the sequencing instruments. Companies like PacBio regularly release instrument improvements, new…

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Thursday, September 6, 2018

New Look at Breast Cancer Cell Line Sheds Light on Structural Complexity

In an exciting paper that made the cover of Genome Research, scientists from Cold Spring Harbor Laboratory and collaborating institutions report the genome sequence and transcriptome of a commonly used breast cancer cell line. They determined that the cell line harbors far more structural variants than previously thought with results that call into question cancer genome analysis based solely on short-read sequencing data. In “Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line,” lead author Maria Nattestad, senior author Michael Schatz, and collaborators describe an in-depth investigation of SK-BR-3, an important…

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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

Justin Zook A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a few individuals, but deeply…

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