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Journal Article

RELACS nuclei barcoding enables high-throughput ChIP-seq

MPS-Authors

Arrigoni,  Laura
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Al-Hasani,  Hoor
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Ramírez,  Fidel
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Panzeri,  Ilaria
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Ryan,  Devon Patrick
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Santacruz,  Diana
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Kress,  Nadia
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Pospisilik,  John Andrew
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Bönisch,  Ulrike
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Manke,  Thomas
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Citation

Arrigoni, L., Al-Hasani, H., Ramírez, F., Panzeri, I., Ryan, D. P., Santacruz, D., et al. (2018). RELACS nuclei barcoding enables high-throughput ChIP-seq. Communications Biology, 214. doi:10.1038/s42003-018-0219-z.


Cite as: https://hdl.handle.net/21.11116/0000-0003-6E45-5
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days.