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
Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo
July 2015
Authors:
Yi-Zhou Jiang, Elisabetta Manduchi, Christian J. Stoeckert, and Peter F. Davies
Info:
In this paper, scientists from the University of Pennsylvania used complete methylated DNA immunoprecipitation sequencing (MeDIP-seq) to study methylation differences in endothelial cells to find clues about atherosclerosis susceptibility. The team used Pippin Prep to size-select MeDIP libraries prior to Illumina sequencing.
Citation:
BMC Genomics 2015, 16:506
doi:10.1186/s12864-015-1656-4
A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost
July 2015
Authors:
Darren Heavens, Gonzalo Garcia Accinelli, Bernardo Clavijo, and Matthew Derek Clark
Info:
Scientists from The Genome Analysis Centre report a protocol using the SageELF to improve library preparation for long mate-pair sequencing. Using a Nextera kit, they show that generating 12 fractions with SageELF saves money and time while requiring less DNA input compared to other gel-based sizing options.
Citation:
BioTechniques 59:42-45 (July 2015)
DOI: 10.2144/000114310