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AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

Sarah Aldridge1, Stephen Watt1, Michael A Quail2, Tim Rayner1, Margus Lukk1, Michael F Bimson3, Daniel Gaffney2 and Duncan T Odom12*

Author Affiliations

1 University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

2 Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK

3 Agilent Technologies UK Limited, Mead Road, Yarnton, Kidlington, Oxfordshire, OX5 1QU, United Kingdom

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Genome Biology 2013, 14:R124  doi:10.1186/gb-2013-14-11-r124

Published: 7 November 2013


ChIP-seq is an established manually-performed method for identifying DNA-protein interactions genome-wide. Here, we describe a protocol for automated high-throughput (AHT) ChIP-seq. To demonstrate the quality of data obtained using AHT-ChIP-seq, we applied it to five proteins in mouse livers using a single 96-well plate, demonstrating an extremely high degree of qualitative and quantitative reproducibility among biological and technical replicates. We estimated the optimum and minimum recommended cell numbers required to perform AHT-ChIP-seq by running an additional plate using HepG2 and MCF7 cells. With this protocol, commercially available robotics can perform four hundred experiments in five days.