Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
March 2014
Authors:
Adam Ameur, Tracy L. Meiring, Ignas Bunikis, Susana Ha¨ggqvist, Cecilia Lindau, Julia Hedlund Lindberg, Inger Gustavsson, Zizipho Z. A. Mbulawa, Anna-Lise Williamson and Ulf Gyllensten
Info:
Researchers at Uppsala University, Sweden, along with the University of Cape Town and the National Health Laboratory in South Africa, examined co-infections in 20 HIV positive women with a rapid detection sequencing method using rolling circle amplification and the Ion Proton platform. The authors indicate a more comprehensive detection when compared to existing genotyping methods, with the added benefit genomic information being collected. The BluePippin was used to size select samples for Proton template generation.
Citation:
Scientific Reports 4:4398
Simultaneous Rapid Sequencing of Multiple RNA Virus Genomes
March 2014
Authors:
John D. Neill, Darrell O. Baylesb, and Julia F. Ridpatha
Info:
Researchers at the USDA in Ames, Iowa, apply NGS to simultaneously sequence ten genomes of archived viruses from a single pooled sample, with the goal of studying viral evolution to facilitate vaccine design. Pippin Prep was used to size select the library pools prior to Ion Torrent sequencing.
Citation:
Journal of Virological Methods (2014)
SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
February 2014
Authors:
Michael A Quail, Miriam Smith, David Jackson, Steven Leonard, Thomas Skelly, Harold P Swerdlow, Yong Gu, and Peter Ellis
Info:
In this paper, scientists from the Wellcome Trust Sanger Institute and Frederick National Laboratory for Cancer Research describe Sample Assurance Spike-In sequencing, or SASI-Seq. The protocol adds uniquely barcoded amplicons to samples prior to library prep and sequencing; these barcodes allow users to deconvolute samples that get mixed up or to spot cross-contamination issues. They used Pippin Prep to test barcode robustness through the size selection process, finding that barcodes were not affected.
Citation:
BMC Genomics, 15:110
Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification
January 2014
Authors:
Peter Tessarz, Helena Santos-Rosa, Sam C. Robson, Kathrine B. Sylvestersen, Christopher J. Nelson1, Michael L. Nielsen and Tony Kouzarides
Info:
The authors describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A. The data suggests that this is the first histone epigenetic mark dedicated to a specific RNA polymerase. Pippin Prep was used to size select ChIP seq libraries prior to Illumina sequencing.
Citation:
Nature, 505 (23) January 2014
Clinical and pathological heterogeneity of a congenital disorder of glycosylation manifesting as a myasthenic/myopathic syndrome
January 2014
Authors:
Dorota M. Monies, Hindi N. Al-Hindi, Mohamed A. Al-Muhaizea, Dyala J. Jaroudi, Banan Al-Younes, Ewa A. Naim, Salma M. Wakil, Brian F. Meyer, Saeed Bohlega
Info:
Collaborators at the King Faisal Specialist Hospital and the Kink Abdulaziz City for Science and Technology, Saudi Arabia, identify an homozygous mutation of ALG2 that is related to congenital muscle weakness disorders. The Pippin Prep was used in sample prep for whole exome sequencing (TargetSeq) on the Ion Torrent Proton
Citation:
Neuromuscul Disord (2014)