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
Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression
March 2012
Authors:
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
Info:
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.
Citation:
Cell Stem Cell 10, 337–344, March 2, 2012
Mutation discovery in mice by whole exome sequencing
December 2011
Authors:
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
Info:
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.
Citation:
Genome Biology 2011, 12:R86