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
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
quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
May 2017
Authors:
Franchini P, Monné Parera D, Kautt AF, Meyer A
Info:
Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method on a population of Neotropical cichlid fish. Pippin Prep was used to size-select fragments prior to Illumina sequencing.
Citation:
Mol Ecol. 2017 May;26(10):2783-2795
doi: 10.1111/mec.14077
Comparative Analysis of Ralstonia solanacearum Methylomes
April 2017
Authors:
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, et al.
Info:
Scientists report results of analyzing epigenetic patterns in two strains of a plant pathogen. They determined that methylation regulates virulence and adaptation to different host plants. BluePippin was used to remove smaller library fragments prior to sequencing with PacBio.
Citation:
Front Plant Sci. 2017; 8: 504
doi: 10.3389/fpls.2017.00504