Citations

Small genomic insertions form enhancers that misregulate oncogenes

February 2017

Authors:
Brian J. Abraham, Denes Hnisz, Abraham S. Weintraub, Nicholas Kwiatkowski, et al.

Info:
In this paper, scientists report using ChIP-seq to better understand the role of non-coding somatic insertions in tumorigenesis. They identified enhancer-associated small insertions, often near oncogenes. Pippin Prep was used in the ChIP-seq protocol to capture 200 bp – 400 bp fragments ahead of sequencing on an Illumina HiSeq 2500.

Citation:
Nature Communications
doi:10.1038/ncomms14385

Posted in Citation | Tagged , , | Comments Off on Small genomic insertions form enhancers that misregulate oncogenes

Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

February 2017

Authors:
Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick, Lúcia G. Lohmann

Info:
Scientists in Michigan and São Paulo, Brazil, performed ddRAD-seq on two separate populations of Amphirrhox longifolia to determine how many SNPs and organisms have to be included for a well-powered study. By resampling the data, they determined that only eight individuals are necessary for studies with at least 1,000 SNPs. The team used Pippin Prep to size fragments for sequencing.

Citation:
Molecular Ecology Resources
DOI: 10.1111/1755-0998.12654

Posted in Citation | Tagged , | Comments Off on Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites

February 2017

Authors:
Aglaia Antoniou, Panagiotis Kasapidis, Georgios Kotoulas, Constantinos C. Mylonas and
Antonios Magoulas

Info:
Scientists from the Hellenic Centre for Marine Research used ddRAD-seq to analyze genome-wide SNPs in the Atlantic Bluefin tuna, with the goal of understanding population structure. Results were inconclusive, suggesting the need for further study. The team used Pippin Prep for the ddRAD-seq protocol.

Citation:
Journal of Biological Research-Thessaloniki
DOI: 10.1186/s40709-017-0062-2

Posted in Citation | Tagged , | Comments Off on Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites

Co-chaperone Hsp70/Hsp90 organizing protein (Hop) is Required for Transposon Silencing and piRNA Biogenesis

February 2017

Authors:
Joseph A. Karam, Rasesh Y. Parikh, Dhananjaya Nayak, David Rosenkranz and Vamsi K. Gangaraju

Info:
Scientists from South Carolina and Mainz, Germany, studied Hop, a co-chaperone that interacts with a piRNA in Drosophila. They found that knocking down Hop activates transposons and that it has an important role in maintaining genome integrity. RNA-seq was performed on an Illumina HiSeq 2500 after Pippin Prep was used for size selection.

Citation:
Journal of Biological Chemistry
doi: 10.1074/jbc.C117.777730

Posted in Citation | Tagged , , , | Comments Off on Co-chaperone Hsp70/Hsp90 organizing protein (Hop) is Required for Transposon Silencing and piRNA Biogenesis

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic

February 2017

Authors:
Etienne Yergeau, Christine Michel, Julien Tremblay, Andrea Niemi, Thomas L. King, Joanne Wyglinski, Kenneth Lee, and Charles W. Greera

Info:
Scientists from Canada and Australia studied how climate change may be affecting microbial communities by performing metagenomic and 16S rRNA gene analysis of bacteria collected from Arctic sea ice and nearby sea water. The different habitats harbored very different microbial populations. Metagenomic sequencing was performed with the Ion Torrent PGM after size selection with the Pippin Prep system.

Citation:
Sci Rep. 2017; 7: 42242

Posted in Citation | Tagged , | Comments Off on Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic