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
A survey of the sorghum transcriptome using single-molecule long reads
June 2016
Authors:
Salah E. Abdel-Ghany, Michael Hamilton, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur & Anireddy S. N. Reddy
Info:
In this publication, scientists from Colorado State University and the National Center for Genome Resources used PacBio sequencing to examine alternative splicing in sorghum. Their transcriptome analysis led to the discovery of thousands of novel splicing events, isoforms, and genes. BluePippin was used to size-select libraries prior to sequencing.
Citation:
Nature Communications
doi:10.1038/ncomms11706
High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
June 2016
Authors:
Jessica L. Preston, Ariel E. Royall, Melissa A. Randel, Kristin L. Sikkink, Patrick C. Phillips, and Eric A. Johnson
Info:
Scientists at the University of Oregon developed a new protocol to reduce sequencing and PCR errors, resulting in more accurate SNP detection even for rare variants. Pippin Prep was used for tight sizing of sequencing libraries prior to paired-end Illumina sequencing.
Citation
BMC Genomics 201617:464
DOI: 10.1186/s12864-016-2669-3