Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress
January 2016
Authors:
B. Shaun Bushman, Keenan L. Amundsen, Scott E. Warnke, Joseph G. Robins, and Paul G. Johnson
Info:
Scientists compared the transcriptomes of two strains of Kentucky bluegrass, one sensitive to salt and the other tolerant even to frequent exposure to salt. cDNA sequencing was performed on an Ion Torrent Proton after library size selection on the BluePippin.
Citation:
BMC Genomics
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
January 2016
Authors:
Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya, Mircea Podar, Christopher Quince and Neil Hall
Info:
Scientists used synthetic metagenomic communities to evaluate the performance of different sequencing and analysis pipelines. They assessed platforms including MiSeq, the PacBio RS II, 454 GS-FLX, and Ion Torrent, and found that sample preparation can alter data interpretation. They used Pippin Prep for sizing NGS libraries prior to sequencing.
Citation:
D’Amore et al. BMC Genomics (2016) 17:55
DOI 10.1186/s12864-015-2194-9
Harnessing the power of RADseq for ecological and evolutionary genomics
January 2016
Authors:
Kimberly R. Andrews, Jeffrey M. Good, Michael R. Miller, Gordon Luikart and Paul A. Hohenlohe
Info:
In this protocol review, scientists examine several approaches to restriction site-associated DNA sequencing and present their findings on how to choose the best method for a specific project. Pippin is included as a key step in the original RADseq protocol.
Citation:
Nature Reviews Genetics
doi:10.1038/nrg.2015.28
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
December 2015
Authors:
Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, et al.
Info:
Scientists from the Jackson Lab and many collaborating institutes used the ChIA-PET strategy with other data sets to understand how genome organization affects transcription in human cells. They analyzed gene expression with the Iso-Seq method on a PacBio system, using SageELF for size selection.
Citation:
Cell 163, 1611–1627
DOI: 10.1016/j.cell.2015.11.024
Population genomics of intrapatient HIV-1 evolution
December 2015
Authors:
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, and Richard Neher
Info:
Researchers from Germany and Sweden sequenced several samples collected over time from each of nine patients with HIV-1 to assess genetic diversity and minor variants of the virus as it evolved. Sequencing was performed on an Illumina MiSeq, with size selection of the Nextera library conducted with BluePippin.
Citation:
eLife 2015;4:e11282
http://dx.doi.org/10.7554/eLife.11282