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
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.
Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples
November 2012
Authors:
Maxime Galan, Marie Pages, Jean-Francois Cosson
Info:
Genotyping rodent strains using targeted NGS of informative regions of cytochrome b and cytochrome c oxidase 1 genes. PCR fragments ~250 bp in length were generated (with barcoded primers) from a variety of sample types, pooled, and size selected as a pool on Pippin Prep to remove non-specific PCR products.
Citation:
PLoS ONE 7(11): e48374. doi:10.1371/journal.pone.0048374
Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation
November 2012
Authors:
Michael A. Quail, Yong Gu, Harold Swerdlow, Matthew Mayho
Info:
An evaluation of semi-automated size selection systems for use in size-selection for NGS libraries at the Sanger Centre. A comparison to manual gel purification and magnetic beads.
Citation:
Electrophoresis: Nov. 2012
The Use of NexGen Sequencing and Junction Sequence Analysis Bioinformatics to Achieve Molecular Characterization of Crops Improved Through Modern Biotechnology
October 2012
Authors:
David Kovalic, Carl Garnaat, Liang Guo, Yongpan Yan, Jeanna Groat, Andre Silvanovich, Lyle Ralston, Mingya Huang, Qing Tian, Allen Christian, Nordine Cheikh, Jerry Hjelle, Stephen Padgette and Gary Bannon
Info:
Materials and Methods: Illumina TruSeq paired-end library generation. Covaris shearing, Pippin Prep size selection at 280 bp. Paired 100 bp reads with indexed adaptors.
Citation:
The Plant Genome: Published online 15 Oct. 2012