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

ABSTRACT: 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.

SUBMITTER: Aldridge S 

PROVIDER: S-EPMC4053851 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

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

Aldridge Sarah S   Watt Stephen S   Quail Michael A MA   Rayner Tim T   Lukk Margus M   Bimson Michael F MF   Gaffney Daniel D   Odom Duncan T DT  

Genome biology 20131107 11

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 recommende  ...[more]

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