Citations

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

Posted in Citation | Tagged | Comments Off on Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

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

Posted in Citation | Tagged , , | Comments Off on The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

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

Posted in Citation | Tagged | Comments Off on Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters

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

Posted in Citation | Tagged , , | Comments Off on Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

June 2017

Authors:

Jason Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au

Info:
In this F1000 publication, scientists describe an evaluation of long-read sequencing technologies, finding that PacBio provides better data quality while Oxford Nanopore generates higher yield. They used SageELF to fractionate cDNAs into four contiguous size ranges.

Citation:
F1000Research 2017, 6:100

Posted in Citation | Tagged , , | Comments Off on Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis