Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles
August 2017
Authors:
Albrecht V, Zweiniger C, Surendranath V, Lang K, et al.
Info:
Scientists in Germany describe a high-throughput approach for characterizing novel HLA alleles. The method involves sequencing the full gene with PacBio and MiSeq. For PacBio sequencing, libraries are sized with BluePippin.
Citation:
HLA. 2017 Aug;90(2):79-87
doi: 10.1111/tan.13057
Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity
July 2017
Authors:
Kelley Yan, Olivier Gevaert, Grace Zheng, Benedict Anchang, et al.
Info:
In this project from scientists at Stanford University School of Medicine and other institutions, comparative RNA-seq was used to analyze putative mouse intestinal stem cells. The team’s findings have implications for cellular plasticity and better understanding stem cells in general. Pippin Prep was used to size libraries before sequencing.
Citation:
Cell Stem Cell
Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice
July 2017
Authors:
Justin Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John Hoidal, and Namakkal Rajasekaran
Info:
Scientists from the University of Alabama at Birmingham and other institutions studied a gene previously associated with oxidative stress, analyzing differential expression in knockout and wild type mouse hearts. They found that the gene may regulate cardiac microRNAs. The team used Pippin Prep to size libraries before sequencing on an Illumina HiSeq.
Citation:
BMC Genomics 2017 18:509
DOI: 10.1186/s12864-017-3875-3
Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis
July 2017
Authors:
Qingshan Xu, Junyan Zhu, Shiqi Zhao, Yan Hou, et al.
Info:
Scientists from Anhui Agricultural University in China performed long-read transcriptome sequencing of the tea plant Camellia sinensis to better understand its production of flavonoids, theanine, and caffeine. They used PacBio sequencing with BluePippin size selection.
Citation:
Front. Plant Sci
doi: 10.3389/fpls.2017.01205
Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing
July 2017
Authors:
Fabio Zanini, Johanna Brodin, Jan Albert, Richard Neher
Info:
Researchers in Germany and Sweden expounded on a previous deep sequencing study of HIV-1 populations to evaluate challenges such as error profiles and proper controls. For the whole genome sequencing, they used BluePippin instead of bead-based sizing to remove inserts shorter than 350 bp to maximize read length on the Illumina MiSeq system.
Citation:
Virus Research, Volume 239, Pages 106-114
doi: 10.1016/j.virusres.2016.12.009