April 2013

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

Authors:
Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson

Info:
The authors use the Pippin Prep as an alternative to gel purification for isolating PCR fragments. The authors note that manual gel purification can lead to underrepresentation of low G+C% sequences.

Citation:PLoS Comput Biol 9(4):e1003031
_____________________________________________________________________

April 2013

Transcriptome Analysis of Thapsia laciniata Rouy Provides Insights into Terpenoid Biosynthesis and Diversity in Apiaceae

Authors:
Damian Paul Drew, Bjørn Dueholm, Corinna Weitzel, Ye Zhang, Christoph W. Sensen, and Henrik Toft Simonsen

Info:
The Pippin Prep was used to size-selec Illumina RNA-seq libraries.

Citation:
Int. J. Mol. Sci. 2013, 14, 9080-9098
_____________________________________________________________________

April 2013

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

Authors:
Jakob Love, Heather A. Hoke, Charles Y. Lin, Ashley Lau, David A. Orlando, Christopher R. Vakoc, James E. Bradner, Tong Ihn Lee, and Richard A. Young

Info:
The Pippin Prep was used to size-selec ChIP-seq libraries.

Citation:Cell 153:320-334 April 2013
_____________________________________________________________________

March/April 2013

H2-Independent Growth of the Hydrogenotrophic Methanogen Methanococcus maripaludis

Authors:
Kyle C. Costa, Thomas J. Lie, Michael A. Jacobs, John A. Leigh

Info:The authors constructed deletions in several key metabolism genes to study the mechanism of H2 independent growth in this hydrogenotropic strain. Several mutants were found that shed new light on alternative mechanisms of methanogenic growth. The mutants were mapped by whole genome sequencing, in which Pippin Prep was used to size selec the libraries.

Citation:mBio (4)2:00062-13 March/April 2013
_____________________________________________________________________

January/February 2013

Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential

Authors:
Ashish Pathak, Stefan J. Green, Andrew Ogram, Ashvini Chauhana

Info:
Rhodococcus strains have diverse and unusual metabolic pathways that are being considered for industrial roles in bioproduction of chemicals and fuels. The authors present the whole genome sequence of one such strain. Nextera chemistry was used with size selection on the Pippin Prep to generate the sequencing libraries.

Citation:genomeA (1)1:e00144-12 January/February 2013
_____________________________________________________________________

January 2013

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing

Authors:
Aylwyn Scally, Bryndis Yngvadottir, Yali Xue, Qasim Ayub, Richard Durbin, Chris Tyler-Smith

Info:
The study used reduced representation libraries to study diversity among the two currently recognized species of gorilla. The libraries were generated by AluI digestion followed by size selection on the Pippin Prep for AluI fragments between 150-250 bp.

Citation:pre-print
_____________________________________________________________________

January 2013

Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene

Authors:
Amanda J. DuBose, Stephen T. Lichtenstein, Narisu Narisu, Lori L. Bonnycastle, Amy J. Swift, Peter S. Chines and Francis S. Collins

Info:
The authors designed a general method to study the arrangement of foreign DNA and host DNA rearrangements in trangenic animals. The protocol involves standard Illumina PE library generation, using the Pippin Prep for size selection, followed by microarray hybridization capture to isolate fragments containing the transgene.

Citation:
Nucleic Acids Research, 2013, 1-5
_____________________________________________________________________

January 2013

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice

Authors:
Jesse N. Weber, Brant K. Peterson & Hopi E. Hoekstra

Info:
The work seeks to identify genetic influences on a complex behavior in mice, burrow formation. The authors used a modified RADseq procedure to genotype two species of wild mice with distinct burrowing behavior. Pippin Prepwas used for size selection in their RADseq protocol.

Citation:Letter, Nature 493:402-405