Citations

Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid

July/August 2016

Authors:
Sean Conlan, Anna F. Lau, NISC Comparative Sequencing Program, Tara N. Palmore, Karen M. Frank, and Julia A. Segre

Info:
NIH scientists sequenced the genome of the first blaNDM-1-positive strain of Klebsiella pneumoniae detected in the institute’s hospital. They found three plasmids, one of which included the blaNDM-1 gene conferring resistance to carbapenems. Sequencing was performed with PacBio, and size selection was done with BluePippin for building long-read libraries.

Citation:
Genome Announc. July/August 2016 vol. 4 no. 4 e00664-16
doi: 10.1128/genomeA.00664-16

Posted in Citation | Tagged , | Comments Off on Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid

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

Posted in Citation | Tagged , , , , | Comments Off on Circulating Extracellular RNA Markers of Liver Regeneration

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

Posted in Citation | Tagged , , | Comments Off on Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

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

Posted in Citation | Tagged , , , , | Comments Off on Genome-wide identification of enhancer elements

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

Posted in Citation | Tagged , , | Comments Off on PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer