The following publications feature the Pippin Platform or have cited its use in methods and materials:
April 2013
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers
Authors:
Jakob Love, Heather A. Hoke, Charles Y. Lin, Ashley Lau, David A. Orlando, Christopher R. Vakoc, James E. Bradner, Tong Ihn Lee, and Richard A. Young
Info:
The Pippin Prep was used to size-select ChIP-seq libraries.
Citation:
Cell 153:320-334 April 2013
http://dx.doi.org/10.1016/j.cell.2013.03.036
_________________________________________________________________________________
March/April 2013
H2-Independent Growth of the Hydrogenotrophic Methanogen Methanococcus maripaludis
Authors:
Kyle C. Costa, Thomas J. Lie, Michael A. Jacobs, John A. Leigh
Info:
The authors constructed deletions in several key metabolism genes to study the mechanism of H2 independent growth in this hydrogenotropic strain. Several mutants were found that shed new light on alternative mechanisms of methanogenic growth. The mutants were mapped by whole genome sequencing, in which Pippin Prep was used to size select the libraries.
Citation:
mBio (4)2:00062-13 March/April 2013
http://dx.doi.org/10.1128/mBio.00062-13
_________________________________________________________________________________
January/February 2013
Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential
Authors:
Ashish Pathak, Stefan J. Green, Andrew Ogram, Ashvini Chauhana
Info:
Rhodococcus strains have diverse and unusual metabolic pathways that are being considered for industrial roles in bioproduction of chemicals and fuels. The authors present the whole genome sequence of one such strain. Nextera chemistry was used with size selection on the Pippin Prep to generate the sequencing libraries.
Citation:
genomeA (1)1:e00144-12 January/February 2013
http://dx.doi.org/10.1128/genomeA.00144-12
_________________________________________________________________________________
January 2013
A genome-wide survey of genetic variation in gorillas using reduced representation sequencing
Authors:
Aylwyn Scally, Bryndis Yngvadottir, Yali Xue, Qasim Ayub, Richard Durbin, Chris Tyler-Smith
Info:
The study used reduced representation libraries to study diversity among the two currently recognized species of gorilla. The libraries were generated by AluI digestion followed by size selection on the Pippin Prep for AluI fragments between 150-250 bp.
Citation:
pre-print
arXiv:1301.1729
_________________________________________________________________________________
January 2013
Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene
Authors:
Amanda J. DuBose, Stephen T. Lichtenstein, Narisu Narisu, Lori L. Bonnycastle, Amy J. Swift, Peter S. Chines and Francis S. Collins
Info:
The authors designed a general method to study the arrangement of foreign DNA and host DNA rearrangements in trangenic animals. The protocol involves standard Illumina PE library generation, using the Pippin Prep for size selection, followed by microarray hybridization capture to isolate fragments containing the transgene.
Citation:
Nucleic Acids Research, 2013, 1-5
doi:10.1093/nar/gks1463
_________________________________________________________________________________
January 2013
Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice
Authors:
Jesse N. Weber, Brant K. Peterson & Hopi E. Hoekstra
Info:
The work seeks to identify genetic influences on a complex behavior in mice, burrow formation. The authors used a modified RADseq procedure to genotype two species of wild mice with distinct burrowing behavior. Pippin Prep was used for size selection in their RADseq protocol.
Citation:
Letter, Nature 493:402-405
doi:10.1038/nature11816
_________________________________________________________________________________
January 2013
A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes(Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq)
Authors:
Hans Recknagel, Kathryn R. Elmer, and Axel Meyer
Info:
RADseq was used to develop linkage maps for two highly divergent Cichlid fish. Pippin Prep was used to size select the libraries.
Citation:
G3 (Bethesda) 3(1):65-74 January 2013
http://dx.doi.org/10.1534/g3.112.003897
_________________________________________________________________________________
December 2012
IL-10 Produced by Induced Regulatory T Cells (iTregs) Controls Colitis and Pathogenic Ex-iTregs during Immunotherapy
Authors:
Erica G. Schmitt, Dipica Haribhai, Jason B. Williams, Praful Aggarwal, Shuang Jia, Louis-Marie Charbonnier, Ke Yan, Rachel Lorier, et al.
Info:
The study included sequencing of the T-cell receptor. For this sequencing, the authors used Ion Torrent platform. The Pippin Prep was used for size-selection as per the standard Life/Ion library construction protocols.
Citation:
J Immunology 189(12): 5638-5648: December 2012
http://dx.doi.org/10.4049/jimmunol.1200936
_________________________________________________________________________________
December 2012
Bactobolin Resistance is Conferred by Mutations in the L2 Ribosomal Protein
Authors:
Josephine Chandler, Thao T. Truong, Patricia M. Silva, Mohammad R. Seyedsayamdost, Galvin Carr, Matthew Radey, Michael A. Jacobs, Elizabeth H. Sims, Jon Clardy, E. Peter Greenberg
Info:
Authors were searching for cause of resistance to antibiotic Bactobolin. Performed Illumina paired-end sequencing on resistant strains. Library construction used size-selection of library on Pippn Prep. Discovery of mutation was straightforward for two of four strains. Other two strains harbored a three base insertion which was not recognized in the initial Illumina sequencing.
Citation:
mBio 3(6):e00499-12: December 2012
http://dx.doi.org/10.1128/mBio.00499-12
_________________________________________________________________________________
November 2012
SATB1-mediated functional packaging of chromatin into loops
Authors:
Terumi Kohwi-Shigematsu, Yoshinori Kohwi, Keiko Takahashi, Hunter W. Richards, Stephen D. Ayers, Hye-Jung Han, Shutao Cai
Info:
Among other things, this paper outlines methods for mapping all DNA binding sites for a global chromatin organizing protein, SATB1. Recombinant HIS-tagged SATB1 protein is incubated with sheared genomic DNA, SATB1 with bound DNA is captured on magnetic HIS particles, and then DNA libraries are prepared from the particle-bound DNA. Illumina library construction is used, with size selection on the Pippin Prep (150-500bp).
Citation:
Methods: November 2012
http://dx.doi.org/10.1016/j.ymeth.2012.06.019,
_________________________________________________________________________________
November 2012
Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism
Authors:
John Archer, Jan Weber, Kenneth Henry, Dane Winner, Richard Gibson, Lawrence Lee, Ellen Paxinos, Eric J. Arts, David L. Robertson, Larry Mimms, Miguel E. Quinones-Mateu
Info:
Comparative study of four NGS platforms (454, Illumina, PacBio, Ion) in clinical assay to determine HIV tropism (polymorphisms in HIV env gene). Ion protocol included amplification ofn 2300 bp env gene fragment, random cleavage, endrepair, adapter ligation, size selection at 150 bp on Pippin Prep, enrichment PCR, library quant., emPCR, sequencing on PGM. All platforms worked almost equally well in this study.
Citation:
PLoS ONE 7(11):e49602.
http://dx.doi.org/10.1371/journal.pone.0049602
_________________________________________________________________________________
November 2012
Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples
Authors:
Maxime Galan, Marie Pages, Jean-Francois Cosson
Info:
Genotyping rodent strains using targeted NGS of informative regions of cytochrome b and cytochrome c oxidase 1 genes. PCR fragments ~250 bp in length were generated (with barcoded primers) from a variety of sample types, pooled, and size selected as a pool on Pippin Prep to remove non-specific PCR products.
Citation:
PLoS ONE 7(11): e48374. doi:10.1371/journal.pone.0048374
http://dx.doi.org/10.1371/journal.pone.0048374
_________________________________________________________________________________
November 2012
Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation
Authors:
Michael A. Quail, Yong Gu, Harold Swerdlow, Matthew Mayho
Info:
An evaluation of semi-automated size selection systems for use in size-selection for NGS libraries at the Sanger Centre. A comparison to manual gel purification and magnetic beads.
Citation:
Electrophoresis: Nov. 2012
http://dx.doi.org/10.1002/elps.201200128
_________________________________________________________________________________
October 2012
The Use of NexGen Sequencing and Junction Sequence Analysis Bioinformatics to Achieve Molecular Characterization of Crops Improved Through Modern Biotechnology
Authors:
David Kovalic, Carl Garnaat, Liang Guo, Yongpan Yan, Jeanna Groat, Andre Silvanovich, Lyle Ralston, Mingya Huang, Qing Tian, Allen Christian, Nordine Cheikh, Jerry Hjelle, Stephen Padgette and Gary Bannon
Info:
Materials and Methods: Illumina TruSeq paired-end library generation. Covaris shearing, Pippin Prep size selection at 280 bp. Paired 100 bp reads with indexed adaptors.
Citation:
The Plant Genome: Published online 15 Oct. 2012
http://dx.doi.org/10.3835/plantgenome2012.10.0026
_________________________________________________________________________________
October 2012
Draft Genome Sequence of Flavobacterium sp. Strain F52, Isolated from the Rhizosphere of Bell Pepper (Capsicum annuum L. cv. Maccabi)
Authors:
Max Kolton, Stefan J. Green, Yael Meller Harel, Noa Sela, Yigal Elad, and Eddie Cytryna
Info:
A brief report of whole genome sequence of a novel Flavobacterium. The bacterial library was created with the EpiCentre Nextera kit. The resulting library was size-selected using broad range size selection, 400-800 bp, on the Pippin Prep before sequencing.
Citation:
Journal of Bacteriology p. 5462–5463 October 2012 Volume 194 Number 19
http://dx.doi.org/10.1128/JB.01249-12
_________________________________________________________________________________
September 2012
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
Authors:
Melissa B. Duhaime, Li Deng, Bonnie T. Poulos, and Matthew B. Sullivan
Info:
A study of most reproducible and sample-efficient methods for sequencing meta-genomic samples with very low abundance samples (20 L ocean water ->1 pg to 1 ng DNA). Detailed side-by-side comparison of standard gel isolation, Pippin Prep, and AMPure bead size selections. The Pippin Prep demonstrated the superior efficiency and reproducibility. Materials and methods: Covaris shearing, end-repair and adapter addition, Pippin size-fractionation, enrichment amplification, sequencing (on 454GLX or Illumina Hi-Seq).
Citation:
Environmental Microbiology (2012) 14(9), 2526–2537
http://dx.doi.org/10.1111/j.1462-2920.2012.02791.x
_________________________________________________________________________________
September 2012
Transcriptional Amplification in Tumor Cells with Elevated c-Myc
Authors:
Charles Y. Lin, Jakob Loven,Peter B. Rahl, Ronald M. Paranal, Christopher B. Burge, James E. Bradner, Tong Ihn Lee, and Richard A. Young
Info:
This high impact study completely revises knowledge on how c-myc gene is involved with gene regulation and cancer. Materials and Methods: Pippin Prep was used for preparation of ChIP-seq. Used multiplexed TruSeq v2 kits. IPDNA end-repaired and A tailed, ligated to adapters, enriched by 18 cycles PCR, then size selected on Pippin to obtain 200-400 bp fragments. Sequenced in single read mode 40b reads, Illumina HiSeq 2000.
Citation:
Cell 151, 56–67, September 28, 2012
http://dx.doi.org/10.1016/j.cell.2012.08.026
_________________________________________________________________________________
September 2012
High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic
Authors:
Rachel Sealfon, Stephen Gire, Crystal Ellis, Stephen Calderwood, Firdausi Qadri, Lisa Hensley, Manolis Kellis, Edward T Ryan, Regina C LaRocque, Jason B Harris, Pardis C Sabeti
Info:
Study performs high-depth NGS on V. cholerae strains from Haiti and DR, some of which had been previously typed by less-thorough PacBio and Illumina studies. Bacterial DNA was fragmented by nebularization, size selected tight at 200bp on Pippin Prep, then prepared library (end-repair, add adapters, enrich PCR for 15 cycles Sequenced on Illumina HiSeq.
Citation:
BMC Genomics 2012, 13:468
http://dx.doi.org/10.1186/1471-2164-13-468
_________________________________________________________________________________
September 2012
Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
Authors:
Marcin Imielinski et al.
Info:
A landmark study of lung cancer genomes with 183 tumor/normal genomes compared. Sequencing was carried out mainly by the Broad Illumina Platform (8 Pippins in production). The Pippin Prep is cited in whole-genome capture section of supplementary methods: DNA sheared, repaired, adaptors added, size selected by manual gels or by Pippin Prep to 340-510 bp. Libraries sequenced in paired end mode on Illumina HiSeq (2x 100 bp reads).
Citation:
Cell 150, 1107–1120, September 14, 2012
http://dx.doi.org/10.1016/j.cell.2012.08.029
_________________________________________________________________________________
August 2012
Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue
Authors:
John D. Morlan, Kunbin Qu, Dominick V. Sinicropi
Info:
After selective depletion of rRNA by RNAse H digestion (following hybridization to rDNA probes), undigested RNA was prepared for NGS sequencing using Illumina TruSeq or Epicentre Script-seq kits. For size-selection steps in the Illumina protocols, Pippin Prep was used for some samples.
Citation:
PLoS ONE 7(8): e42882. doi:10.1371/journal.pone.0042882
http://dx.doi.org/10.1371/journal.pone.0042882
_________________________________________________________________________________
July 2012
Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing
Authors:
Justin M. Zook, Daniel Samarov, Jennifer McDaniel, Shurjo K. Sen, Marc Salit
Info:
New approach to discovery of systematic sequencing errors by use of spike in RNA or DNA control DNAs. Pippin Prep used for RNA-seq library construction. Paired end reads on Illumina GAIIx.
Citation:
PLoS ONE 7(7): e41356.
http://dx.doi.org/10.1371/journal.pone.0041356
_________________________________________________________________________________
May 2012
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
Authors:
Brant K. Peterson, Jesse N. Weber, Emily H. Kay, Heidi S. Fisher, Hopi E. Hoekstra
Info:
An NGS method that allows inexpensive HT genotyping at moderate depth without prior knowledge of any markers. A high impact paper. Extremely reproducible size selection is crucial to the method and the authors used Pippin Prep for this purpose.
Citation:
PLoS ONE 7(5): e37135. doi:10.1371/journal.pone.0037135
http://dx.doi.org/10.1371/journal.pone.0037135
_________________________________________________________________________________
March 2012
Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression
Authors:
Linzhao Cheng, Nancy F. Hansen, Ling Zhao, Yutao Du, Chunlin Zou, Frank X. Donovan, Bin-Kuan Chou, Guangyu Zhou, Shijie Li, Sarah N. Dowey, Zhaohui Ye, NISC Comparative Sequencing Program,
Settara C. Chandrasekharappa, Huanming Yang, James C. Mullikin, and P. Paul Liu
Info:
Whole genome sequencing on reprogrammed stem cell lines. Materials and Methods: Covaris shearing followed by size selection at 450 bp on the Pippin Prep. Illumina TruSeq chemistry on HiSeq 2000, 90 or 101 bp paired end protocols.
Citation:
Cell Stem Cell 10, 337–344, March 2, 2012
http://dx.doi.org/10.1016/j.stem.2012.01.005
_________________________________________________________________________________
December 2011
Mutation discovery in mice by whole exome sequencing
Authors:
Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst,
David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kilew, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham,
Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey Jeddeloh, Jay Shendure and Laura G Reinholdt
Info:
Materials and Methods: Illumina PE libraries were constructed and size selected at 430bp tight on Pippin Prep prior to enrichment PCR and hybridization capture for whole exome regions.
Citation:
Genome Biology 2011, 12:R86
http://dx.doi.org/10.1186/gb-2011-12-9-r86
_________________________________________________________________________________
September 2011
Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn
Authors:
Laura G. Reinholdt, Yueming Ding, Griffith T. Gilbert, Anne Czechanski, Jeffrey P. Solzak, Randall J. Roper, Mark T. Johnson, Leah Rae Donahue, Cathleen Lutz, Muriel T. Davisson
Info:
Illumina PE libraries were constructed and size selected at 400bp tight on Pippin Prep prior to enrichment PCR and hybridization capture for genomic region surrounding the Down syndrome locus in mouse, to identify rearrangements in a much-studied Down’s syndrome model strain.
Citation:
Mamm Genome (2011) 22:685–691