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 () and Ido Amit ()
Additional contact information
Christine S. Cheng: Broad Institute of MIT and Harvard
Kunal Rai: University of Texas MD Anderson Cancer Center
Manuel Garber: Broad Institute of MIT and Harvard
Andrew Hollinger: Broad Institute of MIT and Harvard
Dana Robbins: Broad Institute of MIT and Harvard
Scott Anderson: Broad Institute of MIT and Harvard
Alyssa Macbeth: Broad Institute of MIT and Harvard
Austin Tzou: Broad Institute of MIT and Harvard
Mauricio O. Carneiro: Broad Institute of MIT and Harvard
Raktima Raychowdhury: Broad Institute of MIT and Harvard
Carsten Russ: Broad Institute of MIT and Harvard
Nir Hacohen: Broad Institute of MIT and Harvard
Jeffrey E. Gershenwald: University of Texas MD Anderson Cancer Center
Niall Lennon: Broad Institute of MIT and Harvard
Chad Nusbaum: Broad Institute of MIT and Harvard
Lynda Chin: University of Texas MD Anderson Cancer Center
Aviv Regev: Broad Institute of MIT and Harvard
Ido Amit: Broad Institute of MIT and Harvard

Nature Communications, 2013, vol. 4, issue 1, 1-7

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms3672

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