Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue
John D. Morlan, Kunbin Qu, Dominick V. Sinicropi
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.
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
Justin M. Zook, Daniel Samarov, Jennifer McDaniel, Shurjo K. Sen, Marc Salit
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.
PLoS ONE 7(7): e41356.
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
Brant K. Peterson, Jesse N. Weber, Emily H. Kay, Heidi S. Fisher, Hopi E. Hoekstra
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.
PLoS ONE 7(5): e37135. doi:10.1371/journal.pone.0037135
Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression
Linzhao Cheng, Nancy F. Hansen, Ling Zhao, Yutao Du, Chunlin Zou, Frank X. Donovan, Bin-Kuan Chou, Guangyu Zhou, Shijie Li, Sarah N. Dowey, Zhaohui Ye, NISC Comparative Sequencing Program,
Settara C. Chandrasekharappa, Huanming Yang, James C. Mullikin, and P. Paul Liu
Whole genome sequencing on reprogrammed stem cell lines. Materials and Methods: Covaris shearing followed by size selection at 450 bp on the Pippin Prep. Illumina TruSeq chemistry on HiSeq 2000, 90 or 101 bp paired end protocols.
Cell Stem Cell 10, 337–344, March 2, 2012
Mutation discovery in mice by whole exome sequencing
Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst,
David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kilew, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham,
Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey Jeddeloh, Jay Shendure and Laura G Reinholdt
Materials and Methods: Illumina PE libraries were constructed and size selected at 430bp “tight” setting on Pippin Prep prior to enrichment PCR and hybridization capture for whole exome regions.
Genome Biology 2011, 12:R86