A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems
June 2013
Authors:
Sarah Tulin, Derek Aguiar, Sorin Istrail, and Joel Smith
Info:
Scientists from the Marine Biological Laboratory and Brown University developed a new pipeline for de novo transcriptome assembly that can be used with organisms lacking a well-annotated reference genome. The paper describes library preparation and computational analysis processes. Pippin Prep was used for size selection in a standard Illumina workflow and also in conjunction with an Epicentre ScriptSeq™ kit.
Citation:
EvoDevo 2013 4:16
Phylogeographic Origin of Helicobacter pylori Determines Host-Adaptive Responses upon Coculture with Gastric Epithelial Cells
July 2013
Authors:
Alexander Sheh, Rupesh Chaturvedi, D. Scott Merrell, Pelayo Correa, Keith T. Wilson, James G. Fox
Info:
A study of gene expression comparing several strains of H. pylori. The BluePippin was used to size-select fragments to construct paired-end libraries for Illumina MiSeq.
Citation:
Infection and Immunity, July 2013 Volume 81 Number 7
The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing
June 2013
Authors:
Joseph F. Boland, Charles C. Chung, David Roberson, Jason Mitchell, Xijun Zhang, Kate M. Im, Ji He, Stephen J. Chanock, Meredith Yeager, Michael Dean
Info:
An exome-sequencing study from the NIH comparing Illumina/Nimblegen to Ion Torrent/TargetSeq. Pippin size selection was used for library construction for Ion Proton sequencing.
Citation:
Hum Genet (2013) 132:1153–1163
Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses
Authors:
Sanne P. Smeekens, c Curtis Huttenhower, Anca Riza, Frank L. van de Veerdonk, Patrick L.J.M. Zeeuwen, Joost Schalkwijk, Jos W.M. van der Meer, Ramnik J. Xavier, Mihai G. Netea, Dirk Gevers
Info:
Genomic DNA was subjected to 16S PCR amplifications. Pippin Prep was used to retrieve the amplicons in order to isolate fragments away from aspecific products, prior to Illumina MiSeq sequencing.
Citation:
J Innate Immun
A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology
June 2013
Authors:
A. Murat Eren, Joseph H. Vineis., Hilary G. Morrison, Mitchell L. Sogin
Info:
The authors present a method of library preparation for overlapping paired-end sequencing on the Illumina platform, and improved analysis software, to reduce the error in metagenomic studies using NGS of 16S rRNA gene amplicons. The Pippin Prep was used for DNA size selection.
Citation:
PLoS ONE 8(6): e66643