Monthly Archives: July 2017

Nabsys Returns: CEO Barrett Bready on the Importance of Structural Variation

Posted on July 27, 2017 by Alex

A new podcast from Mendelspod features an interesting interview with Barrett Bready, CEO of electronic mapping firm Nabsys, who emphasizes the growing need to incorporate structural variation data into genome studies. In the discussion, Bready describes his company’s platform, which … more »

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Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

Posted on July 25, 2017 by Alex

August 2017 Authors: Albrecht V, Zweiniger C, Surendranath V, Lang K, et al. Info: Scientists in Germany describe a high-throughput approach for characterizing novel HLA alleles. The method involves sequencing the full gene with PacBio and MiSeq. For PacBio sequencing, … more »

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Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity

Posted on July 25, 2017 by Alex

July 2017 Authors: Kelley Yan, Olivier Gevaert, Grace Zheng, Benedict Anchang, et al. Info: In this project from scientists at Stanford University School of Medicine and other institutions, comparative RNA-seq was used to analyze putative mouse intestinal stem cells. The … more »

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Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice

Posted on July 25, 2017 by Alex

July 2017 Authors: Justin Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John Hoidal, and Namakkal Rajasekaran Info: Scientists from the University of Alabama at Birmingham and other institutions studied a gene previously associated with oxidative stress, analyzing differential expression in … more »

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ddRAD-seq Study Explores Behavioral Roles in Speciation

Posted on July 25, 2017 by Alex

A new preprint from the Hoekstra lab at Harvard makes great use of the double digest RAD-seq protocol to better understand reproductive barriers and speciation in closely related species of mice. Since it was the Hoekstra lab that gave us … more »

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Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

Posted on July 24, 2017 by Alex

July 2017 Authors: Qingshan Xu, Junyan Zhu, Shiqi Zhao, Yan Hou, et al. Info: Scientists from Anhui Agricultural University in China performed long-read transcriptome sequencing of the tea plant Camellia sinensis to better understand its production of flavonoids, theanine, and … more »

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Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

Posted on July 24, 2017 by Alex

July 2017 Authors: Fabio Zanini, Johanna Brodin, Jan Albert, Richard Neher Info: Researchers in Germany and Sweden expounded on a previous deep sequencing study of HIV-1 populations to evaluate challenges such as error profiles and proper controls. For the whole … more »

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For 10x Genomics Workflow, Broad Institute Uses PippinHT Size Selection

Posted on July 18, 2017 by Alex

At the Broad Institute, scientist Michelle Cipicchio is part of the technology development team responsible for optimizing new methods or sample types before they’re implemented on the organization’s industrial-scale exome and whole-genome sequencing pipeline. Recently, she’s been working with the … more »

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PacBio Users: Size Selection Is Essential for Generating Excellent Results

Posted on July 6, 2017 by Alex

The Sage Science team was delighted to attend and co-sponsor PacBio’s annual East Coast user group meeting in Baltimore last week, particularly since there was a half-day session devoted to our favorite subject: sample prep. There were plenty of customer … more »

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