Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path
November 2016
Authors:
Sandra C. Lorenz, Steven R. Monday, Maria Hoffmann, Markus Fischer and Julie A. Kase
Info:
Scientists from the US FDA and the University of Hamburg used PacBio sequencing to characterize plasmids associated with heightened virulence in Shiga toxin-producing E. coli strains. They used BluePippin size selection to produce 20 kb libraries for sequencing.
Citation:
Appl. Environ. Microbiol.
November 2016 vol. 82 no. 216367-6377
Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma
November 2016
Authors:
Ruoyu Zhang, Kiichi Nakahira, Xiaoxian Guo, Augustine M.K. Choi & Zhenglong Gu
Info:
Scientists at Cornell University studied cell-free mitochondrial DNA found in plasma samples collected from sepsis patients. Along the way, they optimized sample prep protocols for short DNA fragments, producing nearly 12 times more fragments in the target size range than standard protocols. They used BluePippin to enrich libraries for fragments of 150 bp to 190 bp.
Citation:
Scientific Reports 6, Article number: 36097 (2016)
doi:10.1038/srep36097
Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
November 2016
Authors:
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, et al.
Info:
Scientists at Ghent University and Baylor College of Medicine evaluated protocols for depleting abundant RNAs from blood and serum samples to improve the ability to detect microRNAs of interest. They found a method that showed success in enriching miRNAs without bias. The team used Pippin Prep to perform size selection of small RNAs.
Citation:
Scientific Reports 6, Article number: 37876 (2016)
doi:10.1038/srep37876
Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome
November 2016
Authors:
Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, et al.
Info:
A large team of scientists in Asia, Europe, and the U.S. collaborated for this study of Tetrahymena thermophile, for which they produced a complete sequence assembly. They also analyzed important genomic features such as rearrangement and evolutionary history. Pippin Prep was used for size selection prior to sequencing on the Illumina HiSeq 2000.
Citation:
eLife
DOI: 10.7554/eLife.19090.001
Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data
September 2016
Authors:
Jianwei Zhang, Ling-Ling Chen, Shuai Sun, et al.
Info:
In this paper, researchers report generating two reference-quality genome assemblies for Oryza sativa subspecies. They publicly released both assemblies, which were built using PacBio and Illumina sequencing technology. For the PacBio work, scientists used BluePippin to size-select 20 kb libraries prior to sequencing.
Citation:
Scientific Data 3, Article number: 160076 (2016)
doi:10.1038/sdata.2016.76