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
Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
September 2012
Authors:
Marcin Imielinski et al.
Info:
A landmark study of lung cancer genomes with 183 tumor/normal genomes compared. Sequencing was carried out mainly by the Broad Illumina Platform (8 Pippins in production). The Pippin Prep is cited in whole-genome capture section of supplementary methods: DNA sheared, repaired, adaptors added, size selected by manual gels or by Pippin Prep to 340-510 bp. Libraries sequenced in paired end mode on Illumina HiSeq (2x 100 bp reads).
Citation:
Cell 150, 1107–1120, September 14, 2012
Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue
August 2012
Authors:
John D. Morlan, Kunbin Qu, Dominick V. Sinicropi
Info:
After selective depletion of rRNA by RNAse H digestion (following hybridization to rDNA probes), undigested RNA was prepared for NGS sequencing using Illumina TruSeq or Epicentre Script-seq kits. For size-selection steps in the Illumina protocols, Pippin Prep was used for some samples.
Citation:
PLoS ONE 7(8): e42882. doi:10.1371/journal.pone.0042882