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
The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly
June 2017
Authors:
An-Yun Chang, Stephane Castel, Evan Ernst, Hyun Soo Kim, Robert Martienssen
Info:
Cold Spring Harbor Laboratory researchers studied the Rct1 protein in S. pombe and found that it is involved in processing pericentromeric transcripts into siRNAs. For the study, small RNA libraries were size-selected on a BluePippin and sequenced on a MiSeq instrument.
Citation:
Cell Reports
Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters
June 2017
Authors:
Kobe Yuen, Brian Slaughter, and Jennifer Gerton
Info:
Scientists in Kansas used the 4C-seq method to study the chromosome complex condensin II in mouse and human genomes. They found that it plays a role in maintaining high expression of histone gene clusters. The team used BluePippin to size-select 4C-seq libraries.
Citation:
Science Advances 21 Jun 2017: Vol. 3, no. 6, e1700191
DOI: 10.1126/sciadv.1700191
Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
June 2017
Authors:
Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Zsolt Balázs, et al.
Info:
Scientists from Hungary and California conducted isoform sequencing with PacBio to analyze the transcriptome of herpes simplex virus type 1. They discovered dozens of previously unidentified protein-coding genes and non-coding RNAs and found that transcription may facilitate crosstalk between distant genes. They used both BluePippin and SageELF to remove shorter fragments and focus libraries on the longest molecules.
Citation:
Front Microbiol. 2017; 8: 1079.
doi: 10.3389/fmicb.2017.01079