Citations

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

March 2016

Authors:
Tomasz Suchan, Camille Pitteloud, Nadezhda S. Gerasimova, Anna Kostikova, Sarah Schmid, Nils Arrigo, Mila Pajkovic, Michał Ronikier, and Nadir Alvarez

Info:
Scientists present a new protocol based on the RAD-seq concept that works more effectively for samples with degraded DNA, such as museum samples. They demonstrate the approach in butterflies and grasshoppers. Pippin Prep was used for size selection of ligation products prior to sequencing.

Citation:
PLoS ONE 11(3): e0151651.
doi:10.1371/journal.pone.0151651

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Identification of Human Islet Amyloid Polypeptide as a BACE2 Substrate

February 2016

Authors:

Ingrid C. Rulifson, Ping Cao, Li Miao, David Kopecky, Linda Huang, Ryan D. White, Kim Samayoa, Jonitha Gardner, Xiaosu Wu, Kui Chen, Trace Tsuruda, Oliver Homann, Helene Baribault, Harvey Yamane, Tim Carlson, Jed Wiltzius, Yang Li

Info:
Researchers from Amgen report on a proteolytic enzyme, BACE2, that could potentially have a therapeutic use for treatment of pancreatic amyloid formation caused by Type-2 diabetes. Illumina RNA-seq, with Pippin size selection, was used to test whether BACE would modulate its target proteins in a cellular setting.

Citation:
PLoS ONE 11(2): e0147254
doi:10.1371/journal.pone.0147254

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Pitfalls of haplotype phasing from amplicon-based long-read sequencing

February 2016

Authors:
Thomas W. Laver, Richard C. Caswell, Karen A. Moore, Jeremie Poschmann, Matthew B. Johnson, Martina M. Owens, Sian Ellard, Konrad H. Paszkiewicz & Michael N. Weedon

Info:
University of Exeter researchers used long-range PCR and long-read sequencing to phase genetic variants separated by 9 Kb, comparing results from the PacBio and Oxford Nanopore sequencing systems. BluePippin was used for size selection of the PacBio 20 Kb library.

Citation:
Scientific Reports 6, Article number: 21746 (2016)
doi:10.1038/srep21746

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Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis

February 2016

Authors:
Andrea D. Tyler, Sara Christianson, Natalie C. Knox, Philip Mabon, Joyce Wolfe, Gary Van Domselaar, Morag R. Graham, and Meenu K. Sharma

Info:
In this PLoS One publication, scientists in Manitoba compare the quality of libraries constructed with Illumina’s Nextera and TruSeq protocols for Mycobacterium tuberculosis, which has a particularly challenging genome. They determined that the TruSeq method yielded more uniform data quality and coverage. BluePippin was used for size selection prior to sequencing on a MiSeq.

Citation:

DOI: 10.1371/journal.pone.0148676

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The Many Dimensions of Diet Breadth: Phytochemical, Genetic, Behavioral, and Physiological Perspectives on the Interaction between a Native Herbivore and an Exotic Host

February 2016

Authors:
Joshua G. Harrison, Zachariah Gompert, James A. Fordyce, C. Alex Buerkle, Rachel Grinstead, Joshua P. Jahner, Scott Mikel, Christopher C. Nice, Aldrin Santamaria, and Matthew L. Forister

Info:
In this study, scientists analyzed butterflies colonizing several different populations of alfalfa, finding significant variation in larval performance between plant groups. Plant DNA was sequenced on an Illumina HiSeq after size selection of library fragments with BluePippin.

Citation:
PLoS One
DOI: 10.1371/journal.pone.0147971

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