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
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
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
Transcriptional Amplification in Tumor Cells with Elevated c-Myc
September 2012
Authors:
Charles Y. Lin, Jakob Loven,Peter B. Rahl, Ronald M. Paranal, Christopher B. Burge, James E. Bradner, Tong Ihn Lee, and Richard A. Young
Info:
This high impact study completely revises knowledge on how c-myc gene is involved with gene regulation and cancer. Materials and Methods: Pippin Prep was used for preparation of ChIP-seq. Used multiplexed TruSeq v2 kits. IPDNA end-repaired and A tailed, ligated to adapters, enriched by 18 cycles PCR, then size selected on Pippin to obtain 200-400 bp fragments. Sequenced in single read mode 40b reads, Illumina HiSeq 2000.
Citation:
Cell 151, 56–67, September 28, 2012
High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic
September 2012
Authors:
Rachel Sealfon, Stephen Gire, Crystal Ellis, Stephen Calderwood, Firdausi Qadri, Lisa Hensley, Manolis Kellis, Edward T Ryan, Regina C LaRocque, Jason B Harris, Pardis C Sabeti
Info:
Study performs high-depth NGS on V. cholerae strains from Haiti and DR, some of which had been previously typed by less-thorough PacBio and Illumina studies. Bacterial DNA was fragmented by nebularization, size selected tight at 200bp on Pippin Prep, then prepared library (end-repair, add adapters, enrich PCR for 15 cycles) and sequenced on Illumina HiSeq.
Citation:
BMC Genomics 2012, 13:468