Citations

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

http://dx.doi.org/10.1371/journal.pone.0048374

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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

http://dx.doi.org/10.1002/elps.201200128

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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

http://dx.doi.org/10.3835/plantgenome2012.10.0026

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Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi)

October 2012

Authors:

Max Kolton, Stefan J. Green, Yael Meller Harel, Noa Sela, Yigal Elad, and Eddie Cytryna

Info:
A brief report of whole genome sequence of a novel Flavobacterium. The bacterial library was created with the EpiCentre Nextera kit. The resulting library was size-selected using broad range size selection, 400-800 bp, on the Pippin Prep before sequencing.

Citation:
Journal of Bacteriology p. 5462–5463 October 2012 Volume 194 Number 19

http://dx.doi.org/10.1128/JB.01249-12

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Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

September 2012

Authors:
Melissa B. Duhaime, Li Deng, Bonnie T. Poulos, and Matthew B. Sullivan

Info:
A study of most reproducible and sample-efficient methods for sequencing meta-genomic samples with very low abundance samples (20 L ocean water ->1 pg to 1 ng DNA). Detailed side-by-side comparison of standard gel isolation, Pippin Prep, and AMPure bead size selections. The Pippin Prep demonstrated the superior efficiency and reproducibility. Materials and methods: Covaris shearing, end-repair and adapter addition, Pippin size-fractionation, enrichment amplification, sequencing (on 454GLX or Illumina Hi-Seq).

Citation:
Environmental Microbiology (2012) 14(9), 2526–2537

http://dx.doi.org/10.1111/j.1462-2920.2012.02791.x

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