Citations

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

March 2017

Authors:
Warren Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, et al.

Info:
Researchers at McGill University and collaborating institutions used ChIP-seq to elucidate the effects of epigenetics and phenotype across the human genome. They analyzed more than 900 samples to understand the effects of epigenetic regulation. The team used Pippin Prep to size-select fragments prior to sequencing on an Illumina HiSeq 2000.

Citation:
Genome Biology (2017) 18:50
DOI 10.1186/s13059-017-1173-7

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Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

March 2017

Authors:
Ryan Collins, Harrison Brand, Claire Redin, Carrie Hanscom, et al.

Info:
Scientists at Harvard and other institutions sequenced nearly 700 individuals with autism spectrum disorder to build a comprehensive map of large structural variants. More than a third of the variants detected are novel. BluePippin was used to size-select libraries prior to library construction for 10x Genomics analysis.

Citation:
Genome Biology (2017) 18:36
DOI 10.1186/s13059-017-1158-6

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Complex multi-enhancer contacts captured by genome architecture mapping

March 2017

Authors:
Robert A. Beagrie, Antonio Scialdone, Markus Schueler, Dorothee Kraemer, et al.

Info:
Scientists in Europe and Canada used a novel approach to characterize genome architecture, analyzing thin sections of the nucleus to spot interactions across large distances in the genome. The method was evaluated in mouse embryonic stem cells. The team used a Pippin Prep to select 300 bp to 500 bp DNA fragments which were sequenced on an Illumina HiSeq.

Citation:
Nature 543, 519–524 (23 March 2017)
doi:10.1038/nature21411

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Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

March 2017

Authors:
Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, et al.

Info:
Scientists from China and the UK scanned the genomes of 352 varieties of cotton, both wild and domestic, to map variants associated with crop domestication throughout its history. They identified 19 candidate variants that may be related to fiber quality. For this project, the team used PippinHT to isolate purified DNA fragments prior to sequencing with an Illumina HiSeq 2000.

Citation:
Nature Genetics 49, 579–587 (2017)
doi:10.1038/ng.3807

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Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere

March 2017

Authors:
Henk J. Schouten, Henri vande Geest, Sofia Papadimitriou, Marian Bemer, Jan G. Schaart, Marinus J. M. Smulders, Gabino Sanchez Perez, Elio Schijlen

Info:
Scientists from Wageningen University and Research sequenced and analyzed several Arabidopsis thaliana plants to understand the mutagenic effects of Agrobacterium tumefaciens. As part of this project, they identified a 50 bp partial T-DNA insert and named it a T-DNA splinter. BluePippin was used to remove short fragments from the library prior to sequencing with PacBio.

Citation:
Plant Cell Reports, volume 36, Issue 3, pp 493–504
DOI: 10.1007/s00299-017-2098-z

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