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
Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing
July 2012
Authors:
Justin M. Zook, Daniel Samarov, Jennifer McDaniel, Shurjo K. Sen, Marc Salit
Info:
New approach to discovery of systematic sequencing errors by use of spike in RNA or DNA control DNAs. Pippin Prep used for RNA-seq library construction. Paired end reads on Illumina GAIIx.
Citation:
PLoS ONE 7(7): e41356.
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
May 2012
Authors:
Brant K. Peterson, Jesse N. Weber, Emily H. Kay, Heidi S. Fisher, Hopi E. Hoekstra
Info:
An NGS method that allows inexpensive HT genotyping at moderate depth without prior knowledge of any markers. A high impact paper. Extremely reproducible size selection is crucial to the method and the authors used Pippin Prep for this purpose.
Citation:
PLoS ONE 7(5): e37135. doi:10.1371/journal.pone.0037135