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
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
Resolving the complexity of the human genome using single-molecule sequencing
November 2014
Authors:
Mark J. P. Chaisson, John Huddleston, Megan Y. Dennis, Peter H. Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano, Jane M. Landolin, John A. Stamatoyannopoulos, Michael W. Hunkapiller, Jonas Korlach & Evan E. Eichler
Info:
In this Nature paper, scientists from the University of Washington, University of Bari Aldo Moro, University of Pittsburgh, and Pacific Biosciences used long-read sequencing to close or shrink 55 percent of gaps remaining in the human reference genome. They detected substantial amounts of structural variation not represented in the current reference. The scientists used BluePippin to prepare 20 Kb and 30 Kb libraries for sequencing (see supplementary info).
Citation:
Nature (2014)
dx.doi.org/10.1038/nature13907