Citations

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

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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

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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.

Citation:
Callicrate et al. BMC Genomics 2014, 15:1098

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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

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CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer

November 2014

Authors:
Edmond Chipumuro, Eugenio Marco, Camilla L. Christensen, Nicholas Kwiatkowski, Tinghu Zhang,Clark M. Hatheway, Brian J. Abraham, Bandana Sharma, Caleb Yeung, Abigail Altabef, Antonio Perez-Atayde, Kwok-Kin Wong, Guo-Cheng Yuan, Nathanael S. Gray, Richard A. Young, and Rani E. George

Info:
Scientists from Harvard and MIT inhibited cyclindependent kinase 7 (CDK7) in neuroblastoma cells and found significant suppression of MYC oncoproteins. In a mouse model, the effect was notable shrinkage of the tumor. Libraries were size-selected for 200 bp to 400 bp using Pippin Prep prior to sequencing on an Illumina HiSeq 2000.

Citation:
Cell (2014)
dx.doi.org/10.1016/j.cell.2014.10.024

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