Citations

A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes(Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)

January 2013

Authors:
Hans Recknagel, Kathryn R. Elmer, and Axel Meyer

Info:
RADseq was used to develop linkage maps for two highly divergent Cichlid fish. Pippin Prep was used to size select the libraries.

Citation:
G3 (Bethesda) 3(1):65-74 January 2013

http://dx.doi.org/10.1534/g3.112.003897

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IL-10 Produced by Induced Regulatory T Cells (iTregs) Controls Colitis and Pathogenic Ex-iTregs during Immunotherapy

December 2012

Authors:
Erica G. Schmitt, Dipica Haribhai, Jason B. Williams, Praful Aggarwal, Shuang Jia, Louis-Marie Charbonnier, Ke Yan, Rachel Lorier, et al.

Info:
The study included sequencing of the T-cell receptor. For this sequencing, the authors used Ion Torrent platform. The Pippin Prep was used for size-selection as per the standard Life/Ion library construction protocols.

Citation:
J Immunology 189(12): 5638-5648: December 2012

http://dx.doi.org/10.4049/​jimmunol.1200936

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Bactobolin Resistance is Conferred by Mutations in the L2 Ribosomal Protein

December 2012

Authors:
Josephine Chandler, Thao T. Truong, Patricia M. Silva, Mohammad R. Seyedsayamdost, Galvin Carr, Matthew Radey, Michael A. Jacobs, Elizabeth H. Sims, Jon Clardy, E. Peter Greenberg

Info:
Authors were searching for cause of resistance to antibiotic Bactobolin. Performed Illumina paired-end sequencing on resistant strains. Library construction used size-selection of library on Pippn Prep. Discovery of mutation was straightforward for two of four strains. Other two strains harbored a three base insertion which was not recognized in the initial Illumina sequencing.

Citation:
mBio 3(6):e00499-12: December 2012

http://dx.doi.org/10.1128/​mBio.00499-12

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SATB1-mediated functional packaging of chromatin into loops

November 2012

Authors:
Terumi Kohwi-Shigematsu, Yoshinori Kohwi, Keiko Takahashi, Hunter W. Richards, Stephen D. Ayers, Hye-Jung Han, Shutao Cai

Info:
Among other things, this paper outlines methods for mapping all DNA binding sites for a global chromatin organizing protein, SATB1. Recombinant HIS-tagged SATB1 protein is incubated with sheared genomic DNA, SATB1 with bound DNA is captured on magnetic HIS particles, and then DNA libraries are prepared from the particle-bound DNA. Illumina library construction is used, with size selection on the Pippin Prep (150-500bp).

Citation:
Methods: November 2012

http://dx.doi.org/10.1016/j.ymeth.2012.06.019,

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Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

November 2012

Authors:
John Archer, Jan Weber, Kenneth Henry, Dane Winner, Richard Gibson, Lawrence Lee, Ellen Paxinos, Eric J. Arts, David L. Robertson, Larry Mimms, Miguel E. Quinones-Mateu

Info:
Comparative study of four NGS platforms (454, Illumina, PacBio, Ion) in clinical assay to determine HIV tropism (polymorphisms in HIV env gene). Ion protocol included amplification of 2300 bp gene fragment, random cleavage, endrepair, adapter ligation, size selection at 150 bp on Pippin Prep, enrichment PCR, library quant., emPCR, sequencing on PGM. All platforms worked almost equally well in this study.

Citation:
PLoS ONE 7(11):e49602.

http://dx.doi.org/10.1371/journal.pone.0049602

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