Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
February 2015
Authors:
Francine E. Garrett-Bakelman, Caroline K. Sheridan, Thadeous J. Kacmarczyk, Jennifer Ishii, Doron Betel, Alicia Alonso, Christopher E. Mason, Maria E. Figueroa, and Ari M. Melnick
Info:
In this publication in the Journal of Visualized Experiments, scientists at Weill Cornell Medical College and the University of Michigan describe a protocol to map DNA methylation patterns across the genome with next-gen sequencing instead of microarrays. Where input amounts allow, the approach calls for automated DNA size selection using Pippin Prep.
Citation:
J Vis Exp. 2015; (96): 52246.
DOI: 10.3791/52246
Assessing the utility of whole genome amplified DNA for next-generation molecular ecology
February 2015
Authors:
Christopher Blair, C. Ryan Campbell, and Anne D. Yoder
Info:
Scientists at Duke University explored whether whole-genome amplification leads to sequence bias by performing a ddRAD-seq study of grey mouse lemurs using multiple displacement amplification. They conclude that MDA enrichment does not cause systematic bias, opening the doors for studies with low-quantity DNA. The team used Pippin Prep for size selection of the ddRAD-seq library.
Citation:
Molecular Ecology Resources (2015) 15, 1079–1090
doi: 10.1111/1755-0998.12376
PU.1 Opposes IL-7–Dependent Proliferation of Developing B Cells with Involvement of the Direct Target Gene Bruton Tyrosine Kinase
December 2014
Authors:
Darah A. Christie, Li S. Xu, Shereen A. Turkistany, Lauren A. Solomon, Stephen K. H. Li, Edmund Yim, Ian Welch, Gillian I. Bell, David A. Hess, and Rodney P. DeKoter
Info:
Scientists from the University of Western Ontario report in this Journal of Immunology paper a research effort to understand how faulty B cell development in mice leads to a form of leukemia. Ultimately, they determined that inducing Btk expression leads to apoptosis, perhaps preventing leukemia formation. Pippin Prep sizing was used for ChIP-seq on an Illumina HiSeq 2000.
Citation:
doi:10.4049/jimmunol.1401569
Genomic resources for the endangered Hawaiian honeycreepers
December 2014
Authors:
Taylor Callicrate, Rebecca Dikow, James W Thomas, James C Mullikin, Erich D Jarvis, Robert C Fleischer1 and NISC Comparative Sequencing Program
Info:
In this BMC Genomics paper, scientists report assembling the genome sequence of Hemignathus virens, a member of the Hawaiian honeycreeper bird family. They identified nearly 4 million SNPs in the genome, as well as some 156,000 SNPs in a RAD tag study of five honeycreeper species that were compared to the reference genome assembly. Paired-end sequencing was perfomed with the MiSeq and HiSeq 2000 after size selection with Pippin Prep.
Computational and Statistical Analyses of Insertional Polymorphic Endogenous Retroviruses in a Non-Model Organism
November 2014
Authors:
Le Bao, Daniel Elleder, Raunaq Malhotra, Michael DeGiorgio, Theodora Maravegias,
Lindsay Horvath, Laura Carrel, Colin Gillin, Tomáš Hron, Helena Fábryová, David R. Hunter and Mary Poss
Info:
Scientists present a computational method for detecting specific integration sites of endogenous retroviruses in a genome, even without the use of a reference genome. They use de novo clustering and statistical models and demonstrate the approach in a study of deer. Pippin Prep sizing was used to narrow the fragment size range to 300-330bp prior to sequencing on the Ion Personal Genome Machine.
Citation:
Computation 2014, 2, 221-245
doi:10.3390/computation2040221