Tag Archives: Pippin System

Publication: Spike-In Standards for Managing Systematic Sequencing Errors

Posted on August 28, 2012 by Alex

Here’s a paper worth checking out: “Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing” from lead author Justin Zook at the National Institute of Standards and Technology. Published in PLoS One last month, the paper … more »

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Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

Posted on August 23, 2012 by Alex

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. … more »

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For NRC Team, Pippin Platform Leads to Higher-Quality Assemblies

Posted on July 24, 2012 by Alex

At the DNA Technologies Laboratory at the National Research Council of Canada, scientists are using the Pippin size selection platform to improve the quality of their genome assemblies. Andrew Sharpe, Research Officer and Group Leader of the Saskatoon-based laboratory, got … more »

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Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

Posted on July 23, 2012 by Alex

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 … more »

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Broad Institute Teams with Sage Science for Automated Sizing

Posted on June 20, 2012 by Alex

Don’t miss this great blog post from the Broad Institute (“A Sage partnership”) describing collaborative work between their genome sequencing team and Sage Science to design a better size selection process for the Broad’s sequencing pipeline. Headed up by Sheila … more »

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New Cassettes Use Internal Standards

Posted on April 27, 2012 by Alex

We’ve just released new dye-free cassettes for the BluePippin and Pippin Prep that use dye-labeled DNA markers* as internal standards, instead of typical external marker set. In the new product, the labeled markers will come premixed wi th the Ficoll … more »

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Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression

Posted on March 23, 2012 by Alex

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, … more »

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Mutation discovery in mice by whole exome sequencing

Posted on December 23, 2011 by Alex

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 … more »

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Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn

Posted on September 1, 2011 by Alex

September 2011 Authors: Laura G. Reinholdt, Yueming Ding, Griffith T. Gilbert, Anne Czechanski, Jeffrey P. Solzak, Randall J. Roper, Mark T. Johnson, Leah Rae Donahue, Cathleen Lutz, Muriel T. Davisson Info: Illumina PE libraries were constructed and size selected at … more »

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ChIP-Seq sample prep tip – Interpreting the apparent presence of a secondary band in size-selected DNA

Posted on June 14, 2011 by Alex

ChIP-Seq analysis is used to study the control of gene expression by identifying DNA regions that are associated  with chromatin at the time of cellular analysis. The ChIP-Seq procedure typically involves cross-linking DNA to the associated chromatin proteins, sonication to … more »

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