A genomic selection component analysis characterizes migration-selection balance
July 2015
Authors:
Patrick J. Monnahan, Jack Colicchio, and John K. Kelly
Info:
In the journal Evolution, scientists from the University of Kansas report the population study of a plant species in novel habitat, which allowed them to carefully monitor genetic evolution. They found indications of gene flow, and observed as the population’s genome altered from existing populations in other habitats. They used Pippin Prep for size selection.
Citation:
DOI: 10.1111/evo.12698
Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath
July 2015
Authors:
Sandeep K. Kasoji, Samantha G. Pattenden, Ewa P. Malc, Chatura N. Jayakody, James K. Tsuruta, Piotr A. Mieczkowski, William P. Janzen, Paul A. Dayton
Info:
This paper from researchers at the University of North Carolina describes the use of nanodroplets to facilitate fragmentation of DNA in an ultrasonic water bath, instead of high-end acoustic sonication instruments. The team used Pippin Prep size selection in their library prep.
Citation:
PLoS One
DOI: 10.1371/journal.pone.0133014
KRAS-dependent sorting of miRNA to exosomes
July 2015
Authors:
Diana J Cha, Jeffrey L Franklin, Yongchao Dou, Qi Liu, James N Higginbotham, Michelle Demory Beckler, Alissa M Weaver, Kasey Vickers, Nirpesh Prasad, Shawn Levy, Bing Zhang, Robert J Coffey, and James G Patton
Info:
Scientists from Vanderbilt University and the HudsonAlpha Institute for Biotechnology studied exosomes released by colorectal cancer cells with mutated KRAS, finding that exosomal miRNAs can function in target cells and that exosomal profiles are different from cellular profiles. Pippin Prep was used to select small RNAs, and sequencing was performed on an Illumina HiSeq.
Citation:
eLife 2015;4:e07197
DOI: http://dx.doi.org/10.7554/eLife.07197
EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing
August 2015
Authors:
Drew R. Schield, Matthew R. Walsh, Daren C. Card, Audra L. Andrew, Richard H. Adams and Todd A. Castoe
Info:
University of Texas researchers present a new method for quantifying methylation patterns across whole genomes at low cost. EpiRADseq is based on the ddRAD-seq protocol and uses a restriction enzyme that’s sensitive to methylation. DNA sizing is performed with an automated Pippin system.
Citation:
Methods in Ecology and Evolution
Volume 7, Issue 1, pages 60–69
Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing
July 2015
Authors:
Juan Pablo Lopez, Alpha Diallo, Cristiana Cruceanu, Laura M. Fiori, Sylvie Laboissiere, Isabelle Guillet, Joelle Fontaine, Jiannis Ragoussis, Vladimir Benes, Gustavo Turecki, and Carl Ernst
Info:
Scientists from McGill University and the European Molecular Biology Laboratory evaluated a number of methods used to discover small, noncoding RNAs in an Illumina workflow. As part of the project, they reviewed library prep protocols, including the Pippin Prep.
Citation:
BMC Medical Genomics 2015, 8:35
doi:10.1186/s12920-015-0109-x