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Tag Archives: Methods
DSBCapture: in situ capture and sequencing of DNA breaks
August 2016 Authors: Stefanie V Lensing, Giovanni Marsico, Robert Hänsel-Hertsch, Enid Y Lam, David Tannahill & Shankar Balasubramanian Info: Scientists at Cancer Research UK developed and validated a new sequencing-based protocol to spot double-stranded DNA breaks in situ; these regions … more »
Posted in Citation
Tagged BluePippin, DNA Sequencing, Illumina, Methods, NextSeq
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RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data
August 2016 Authors: Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC Info: In this methods paper, scientists combine double-digest RAD-seq with capture technology to reduce costs and increase efficiency. The protocol, which was validated … more »
Posted in Citation
Tagged ddRADseq, genotyping, Illumina, Methods, NextSeq, Pippin Prep, Target Enrichment
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Genome-wide identification of enhancer elements
June 2016 Authors: Sarah Tulin, Julius C. Barsi, Carlo Bocconcelli, and Joel Smith Info: The authors (from Woods Hole and Cal Tech) present a genome-wide regulatory element database for the sea urchin embryo. To do this, they developed a new … more »
PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
Scientists at the University of Oregon have published a new method to detect PCR and sequencing errors that should help other researchers track rare SNPs with greater accuracy. PELE-seq, which gets our vote for best new protocol name, can be … more »
Posted in Blog
Tagged ddRADseq, genotyping, HiSeq, Illumina, Methods, Pippin Prep
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Double Pippin for Optimized RAD-seq
Scientists in China and the UK recently published an open-access optimized protocol for RAD-seq in the Theoretical and Applied Genetics journal. The method is targeted at large studies of plants and enables users to specify sequence coverage parameters. From lead … more »
New hyRAD Method Expands Use of RAD-seq to Degraded Samples
Since RAD-seq was first developed, we’ve seen a number of new versions and approaches from an enthusiastic scientific community. The latest was recently published in PLoS One and demonstrates a RAD-based method suitable for analyzing degraded DNA, an essential step … more »
Posted in Blog
Tagged genotyping, Illumina, Methods, MiSeq, Pippin Prep, RAD-seq
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A method to simultaneously construct up to 12 differently sized Illumina Nextera long mate pair libraries with reduced DNA input, time, and cost
July 2015 Authors: Darren Heavens, Gonzalo Garcia Accinelli, Bernardo Clavijo, and Matthew Derek Clark Info: Scientists from The Genome Analysis Centre report a protocol using the SageELF to improve library preparation for long mate-pair sequencing. Using a Nextera kit, they … more »
Scientists Optimize Mate-Pair Sequencing with SageELF
In a Biotechniques paper this month, scientists from The Genome Analysis Centre describe a new method for mate-pair sequencing that saves time and money while decreasing the amount of input DNA required. The method is based on SageELF, which automatically … more »
Posted in Blog
Tagged BluePippin, Methods, SageELF, TGAC
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Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents
June 2014 Authors: S Timothy Motley, John M Picuri, Chris D Crowder, Jeremiah J Minich, Steven A Hofstadler and Mark W Eshoo Info: In this methods paper, researchers from Ibis Biosciences report a superior whole-genome amplification protocol that can be … more »
Posted in Citation
Tagged Ion Torrent, Methods, Pippin Prep
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Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma
June 2014 Authors: Kristina Warton, Vita Lin, Tina Navin, Nicola J Armstrong, Warren Kaplan, Kevin Ying, Brian Gloss, Helena Mangs, Shalima S Nair, Neville F Hacker, Robert L Sutherland, Susan J Clark and Goli Samimi1 Info: This study from the … more »
Posted in Citation
Tagged Featured, Illumina, Methods, Pippin Prep
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