Circulating Extracellular RNA Markers of Liver Regeneration
July 2016
Authors:
Irene K. Yan, Xue Wang, Yan W. Asmann, Hiroaki Haga, Tushar Patel
Info:
Mayo Clinic researchers performed partial hepatectomies in mice and then monitored RNA activity in serum samples to find a signature associated with liver regeneration. They found detectable changes in small non-coding RNAs such as microRNA, snoRNA, tRNA, and more. The team used Pippin Prep to fractionate RNA libraries prior to sequencing with Illumina MiSeq.
Citation:
PLoS ONE 11(7): e0155888.
doi:10.1371/journal.pone.0155888
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads
July 2016
Authors:
Jiaqiang Dong, Yaping Feng, Dibyendu Kumar, Wei Zhang, Tingting Zhu, Ming-Cheng Luo, and Joachim Messing
Info:
Scientists from Rutgers University and the University of California, Davis, analyzed copy number variation in the highly repetitive maize genome using PacBio sequencing. They used BluePippin to build 20 Kb libraries.
Citation:
PNAS
DOI 10.1073/pnas.1608775113
Genome-wide identification of enhancer elements
June 2016
Authors:
Sarah Tulin, Julius C. Barsi, Carlo Bocconcelli, and Joel Smith
Info:
The authors (from Woods Hole and Cal Tech) present a genome-wide regulatory element database for the sea urchin embryo. To do this, they developed a new method, GRIP-seq, that combines elements of conformation capture, ChIP, and paired-end sequencing. Pippin Prep size selection was used with the Nextera library kit for the ChIP library construction process.
Citation:
Int. J. Dev. Biol. 60: 141-150 (2016)
doi: 10.1387/ijdb.160108jb
PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer
June 2016
Authors:
Jennifer M. Spangle, Koen M. Dreijerink, Anna C. Groner, Hailing Cheng, Carolynn E. Ohlson, Jaime Reyes, Charles Y. Lin, James Bradner, Jean J. Zhao, Thomas M. Roberts, and Myles Brown
Info:
In this breast cancer research study, scientists evaluate the PI3K/AKT signaling pathway on the epigentic methylation of the H3 histone in cells which is implicated in cell growth for late stage cancers. They suggest that the H3K4 gene may be useful epigenetic markers for PI3K/AKT inhibitors in clinical development. Pippin Prep was used for the ChIP-seq size selection.
This study was a collaboration with the Dana Farber Cancer Institute, Harvard Medical School, and The Second Hospital of Dalian Medical University, China.
Citation:
Cell Reports 15, 2692–2704
doi.org/10.1016/j.celrep.2016.05.046
Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
June 2016
Authors:
Shruthi Sridhar Vembar, Matthew Seetin, Christine Lambert, Maria Nattestad, Michael C. Schatz, Primo Baybayan, Artur Scherf, and Melissa Laird Smith
Info:
Scientists in France and the US used PacBio sequencing to characterize the AT-rich genome of this deadly malaria parasite. Half of all sequence reads were longer than 15.5 Kb, allowing the scientists to produce an assembly with each chromosome fully resolved. They used BluePippin to eliminate fragments smaller than 15 Kb and Pippin Pulse to assess size distribution of sheared DNA.
Citation:
DNA Res (2016)
doi: 10.1093/dnares/dsw022