August 2013

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Authors:
Stephen M Gross, Jeffrey A Martin, June Simpson, María Jazmín Abraham-Juarez, Zhong Wang and Axel Visel

Info:
Agave is an interesting plant for bioenergy study. This paper provides transcriptome data of two strains. The Pippin Prep was used to size selec cDNAs at 250 or 500 bp, followed by TrueSeq library construction and sequencing on the Illumina HiSeq.

Citation:BMC Genomics 2013 14:563
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August 2013

Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association

Authors:
Nandan P Deshpande, Nadeem O Kaakoush, Marc R Wilkins and Hazel M Mitchell

Info:
Collaborators at the University of New South Wales sequence several strains of Campylobacter concisus from healthy and diseased (Crohn’s disease and gastroenteritis) individuals for a comparative study. Results showed genetice diversity and identified pathways that may be associated with the diseases. Pippin Prep was used to size selec libraries for Illumina HiSeq.

Citation:BMC Genomics 2013 14:585
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July 2013

Phylogeographic Origin of Helicobacter pylori Determines Host-Adaptive Responses upon Coculture with Gastric Epithelial Cells

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-selec fragments to construct paired-end libraries for Illumina MiSeq.

Citation:Infection and Immunity, July 2013 Volume 81 Number 7
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June 2013

The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

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
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June 2013

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
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June 2013

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

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
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May 2013

Characterizing and measuring bias in sequence data

Authors:
Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum and David B Jaffe

Info:
Researchers at the Broad Institute compare sequence bias on Illumina, Ion, PacBio, and Complete Genomics platforms. Pippin sizing was used on the Ion Torrent libraries. The authors note that library construction conditions significantly influence sequencing bias.

Citation:Genome Biology 2013, 14:R51
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May 2013

Deciphering the Growth Behaviour of Mycobacterium africanum

Authors:
Florian Gehre, Jacob Otu, Kathryn DeRiemer, Paola Florez de Sessions, Martin L. Hibberd, Wim Mulders, Tumani Corrah, Bouke C. de Jong, Martin Antonio

Info:
The Pippin Prep was used to size selec libraries prepared with the New England Biolabs NEB Next DNA sample prep kit. DNA was sequenced on the Illumina HiSeq 2000.

Citation:PLoS Negl Trop Dis 7(5): e2220