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
Towards allele-level human leucocyte antigens genotyping – assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq
June 2015
Authors:
J. L. Duke, C. Lind, K. Mackiewicz, D. Ferriola, A. Papazoglou, O. Derbeneva, D. Wallace, and D. S. Monos
Info:
This publication in the International Journal of Immunogenetics from scientists at the Children’s Hospital of Philadelphia presents an assessment of the Ion Torrent PGM and Illumina MiSeq for HLA typing as well as detailed workflows for each. DNA sizing for both instruments was performed with Pippin Prep.
Citation:
DOI: 10.1111/iji.12213
Assembly and diploid architecture of an individual human genome via single-molecule technologies
June 2015
Authors:
Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, Ajay Ummat, Oscar Franzen, Tobias Rausch, Adrian M Stütz, William Stedman, Thomas Anantharaman, Alex Hastie, Heng Dai, Markus Hsi-Yang Fritz, Han Cao, Ariella Cohain, Gintaras Deikus, Russell E Durrett, Scott C Blanchard, Roger Altman, Chen-Shan Chin, Yan Guo, Ellen E Paxinos, Jan O Korbel, Robert B Darnell, W Richard McCombie, Pui-Yan Kwok, Christopher E Mason, Eric E Schadt & Ali Bashir
Info:
Scientists report “the first comprehensive analysis of a diploid human genome” generated by long-read sequencing and single-molecule genome maps. The resulting hybrid assembly dramatically increased contiguity, with scaffold N50s nearly 30 Mb. BluePippin was used to remove DNA fragments shorter than 7 Kb prior to PacBio sequencing.
Citation:
Nature Methods.
DOI:10.1038/nmeth.3454
Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes
June 2015
Authors:
Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela, and Matthew K. Fujita
Info:
In this paper, scientists in Texas and Mexico challenge conventional climate-based species boundaries in the speckled rattlesnake, using genomic and other data to support their recommendation that three current subspecies should be recognized as independent species. They used ddRAD-seq with BluePippin size selection to provide genotyping data for the snakes.
Citation:
PLoS ONE 10(6): e0131435.
doi:10.1371/journal.pone.0131435