SimRAD: a R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
May 2014 (epub ahead of print)
Authors:
Olivier Lepais and Jason T Weir
Info:
This article from Molecular Ecology Resources describes a new software tool designed to help scientists optimize their double-digest RADseq (ddRADseq) experiments by accurately estimating the number of loci generated by a particular method. The tool uses a reference genome to approximate the organism of interest and predicts the number of loci for various protocols, such as tight versus wide size selection with the Pippin Prep.
Citation:
Molecular Ecology Resources 2014
Quality control of next-generation sequencing data without a reference
May 2014
Authors:
Urmi H Trivedi, Timothée Cézard, Stephen Bridgett, Anna Montazam, Jenna Nichols, Mark Blaxter, and Karim Gharbi
Info:
In this paper published in Frontiers in Genetics, scientists at the University of Edinburgh show that it is possible to perform alignment-based quality control on sequence data for organisms that lack a reference genome. They used draft assemblies for organisms representing various genome sizes and found that useful quality control metrics can be inferred from these drafts. The scientists used Illumina sequencing and performed DNA sizing with BluePippin.
Citation:
Front. Genet. 5:111
Highly Specific Contractions of a Single CAG/CTG Trinucleotide Repeat by TALEN in Yeast
April 2014
Authors:
Guy-Franck Richard, David Viterbo, Varun Khanna, Valentine Mosbach, Lauriane Castelain, and Bernard Dujon
Info:
Researchers in France used a TALEN to introduce a double-strand break in a CAG/CCTG repeat in yeast cells, finding that doing so deleted the trinucleotide repeat tract or shortened highly repetitive regions into relatively few repeats. This PLoS One paper is the first evidence of deploying a TALEN to shorten trinucleotide repeats, which in humans are responsible for many severe neurological disorders. DNA was fractionated with Pippin Prep and sequenced with Illumina.
Citation:
PLoS ONE 9(4): e95611
The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure
April 2014
Authors:
Sateesh Kagale, Chushin Koh, John Nixon, Venkatesh Bollina, Wayne E. Clarke, Reetu Tuteja, Charles Spillane, Stephen J. Robinson, Matthew G. Links, Carling Clarke, Erin E. Higgins, Terry Huebert, Andrew G. Sharpe & Isobel A.P. Parkin
Info:
Scientists in Canada and Ireland generated a genome sequence of Camelina sativa and annotated more than 89,000 protein-coding genes for the oilseed crop. They determined that C. sativa experienced a whole-genome triplication that may suggest hybridization between different ancestral species with lower numbers of chromosomes. Sequencing was performed with the Illumina HiSeq after Pippin Prep size selection and with the Roche 454 FLX Titanium sequencer.
Citation:
Nature Communications 5:3706
The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells
March 2014
Authors:
Makoto Kurachi, R Anthony Barnitz, Nir Yosef, Pamela M Odorizzi, Michael A DiIorio, Madeleine E Lemieux, Kathleen Yates, Jernej Godec, Martin G Klatt, Aviv Regev, E John Wherry and W Nicholas Haining
Info:
Collaborators led by scientists at Upenn’s Perelman School of Medicine and The Dana-Farber Cancer Institute show that BATF is a central regulator of early differentiation of CD8+ Tcells. Pippin Prep was used to size select Illumina libraries in a ChIP-Seq workflow.
Citation:
Nature Immunology15:4 (2014)