Semiconductor-based DNA sequencing of histone modification states

Christine S. Cheng; Kunal Rai; Manuel Garber; Andrew Hollinger; Dana Robbins; Scott Anderson; Alyssa Macbeth; Austin Tzou; Mauricio O. Carneiro; Raktima Raychowdhury; Carsten Russ; Nir Hacohen; Jeffrey E. Gershenwald; Niall Lennon; Chad Nusbaum; Lynda Chin; Aviv Regev; Ido Amit

doi:10.1038/ncomms3672

Semiconductor-based DNA sequencing of histone modification states

Christine S. Cheng, Kunal Rai, Manuel Garber, Andrew Hollinger, Dana Robbins, Scott Anderson, Alyssa Macbeth, Austin Tzou, Mauricio O. Carneiro, Raktima Raychowdhury, Carsten Russ, Nir Hacohen, Jeffrey E. Gershenwald, Niall Lennon, Chad Nusbaum, Lynda Chin, Aviv Regev, Ido Amit

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10 Scopus citations

Abstract

The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.

Original language	English (US)
Article number	2672
Journal	Nature communications
Volume	4
DOIs	https://doi.org/10.1038/ncomms3672
State	Published - Oct 25 2013

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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Clinical Trials Office

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Cheng, C. S., Rai, K., Garber, M., Hollinger, A., Robbins, D., Anderson, S., Macbeth, A., Tzou, A., Carneiro, M. O., Raychowdhury, R., Russ, C., Hacohen, N., Gershenwald, J. E., Lennon, N., Nusbaum, C., Chin, L., Regev, A., & Amit, I. (2013). Semiconductor-based DNA sequencing of histone modification states. Nature communications, 4, Article 2672. https://doi.org/10.1038/ncomms3672

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abstract = "The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.",

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AU - Rai, Kunal

AU - Garber, Manuel

AU - Hollinger, Andrew

AU - Robbins, Dana

AU - Anderson, Scott

AU - Macbeth, Alyssa

AU - Tzou, Austin

AU - Carneiro, Mauricio O.

AU - Raychowdhury, Raktima

AU - Russ, Carsten

AU - Hacohen, Nir

AU - Gershenwald, Jeffrey E.

AU - Lennon, Niall

AU - Nusbaum, Chad

AU - Chin, Lynda

AU - Regev, Aviv

AU - Amit, Ido

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Semiconductor-based DNA sequencing of histone modification states

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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