Citations

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

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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

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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

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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

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Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolaceaS4054 Lacking the Malic Enzyme

September 2016

Authors:
Mariane S. Thøgersen, Marina W. Delpin, Jette Melchiorsen, Mogens Kilstrup, Maria Månsson, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Kristian F. Nielsen, and Lone Gram

Info:
A team of scientists analyzed biological compounds produced by Pseudoalteromonas luteoviolacea, a marine bacterium. They determined that the compounds, suspected to have antibacterial activity, were not effective in that role and that the bacterium may be producing other undiscovered compounds that achieve this function. Sequencing was conducted with PacBio after size-selection with BluePippin for 10 kb libraries.

Citation:
Front Microbiol. 2016; 7: 1461.
doi: 10.3389/fmicb.2016.01461

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