Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing
May 2015
Authors:
Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, and Shigehiro Kuraku
Info:
Scientists from RIKEN modified the recommended protocol for the Nextera Mate Pair Sample Prep Kit from Illumina to improve library yield and quality while minimizing cost. Changes included optimizing tagmentation conditions, intensive shearing of DNA, and more. The team also switched the order of size selection, using BluePippin before the strand displacement reaction, which saves money by reducing reagent volumes.
Citation:
BioTechniques 58:253-257 (May 2015)
doi 10.2144/000114288
Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies
April 2015
Authors:
Sagar M Utturkar, Dawn M Klingeman, José M Bruno-Barcena, Mari S Chinn, Amy M Grunden, Michael Köpke & Steven D Brown
Info:
Researchers from the University of Tennessee, North Carolina State University, and other organizations present data from four different sequencing platforms to elucidate the microbe and to provide a community resource for platform comparisons. PacBio libraries were size-selected with BluePippin.
Citation:
Scientific Data
doi:10.1038/sdata.2015.14
Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms
April 2015
Authors:
Hans Recknagel, Arne Jacobs, Pawel Herzyk, Kathryn R Elmer
Info:
In this Molecular Ecology Resources paper, researchers from the University of Glasgow describe a protocol and adapters they developed for double-digest RAD sequencing on the Ion Torrent platform. They found that ddRADseq-ion’s strongest applications are pilot assessments and quick data return. They used Sage Pippin Prep to perform individual size selection from multiplexed libraries.
Citation:
doi: 10.1111/1755-0998.12406
Assessing structural variation in a personal genome—towards a human reference diploid genome
April 2015
Authors:
Adam C English, William J Salerno, Oliver A Hampton, Claudia Gonzaga-Jauregui, Shruthi Ambreth, Deborah I Ritter, Christine R Beck, Caleb F Davis, Mahmoud Dahdouli, Singer Ma, Andrew Carroll, Narayanan Veeraraghavan, Jeremy Bruestle, Becky Drees, Alex Hastie, Ernest T Lam, Simon White, Pamela Mishra, Min Wang, Yi Han, Feng Zhang, Pawel Stankiewicz, David A Wheeler, Jeffrey G Reid, Donna M Muzny, Jeffrey Rogers, Aniko Sabo, Kim C Worley, James R Lupski, Eric Boerwinkle and Richard A Gibbs
Info:
In this BMC Genomics paper, scientists characterize structural variation across a human genome using Parliament, a new structural variant-calling pipeline developed at Baylor. They found that long reads are critical to detecting structural variants. BluePippin was used to prepare 20 Kb libraries for the PacBio sequencer.
Citation:
BMC Genomics 2015, 16:286
doi:10.1186/s12864-015-1479-3
Improved transposon-based library preparation for the Ion Torrent platform
April 2015
Authors:
Tatyana Gorbacheva, Wilber Quispe-Tintaya, Vasily N. Popov, Jan Vijg, and Alexander Y. Maslov
Info:
In this Biotechniques paper, scientists from the Albert Einstein College of Medicine in New York describe MuPlus, a new transposon-based method for barcoded library prep compatible with Ion Torrent sequencers. The protocol eliminates self-complementary regions, increasing sequencing efficiency. Pippin Prep was used for automated size selection of a mouse library.
Citation:
BioTechniques, Vol. 58, No. 4, April 2015, pp. 200–202