A protocol for high-throughput microplate-based CUT&Tag

Johnson, B. B.; Boyle, G. E.; Federico, A. J.; Ma, J.; Hemani, H.; Spencer, D. H.; Sarthy, J. F.; Meers, M. P.

doi:10.1101/2025.09.18.676951

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bioRxiv · 10.1101/2025.09.18.676951

A protocol for high-throughput microplate-based CUT&Tag

Johnson, B. B.·Boyle, G. E.·Federico, A. J.·Ma, J.·Hemani, H.·Spencer, D. H.·Sarthy, J. F.·Meers, M. P.

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Abstract

Cleavage Under Targets & Tagmentation (CUT&Tag) is a versatile method for measuring genomic occupancy of chromatin-associated proteins with high sensitivity and specificity. CUT&Tag has low sequencing requirements and is therefore suitable for highly multiplexed experiments, but methods to process samples at throughput without specialized equipment are lacking. Here we present a method for simultaneous parallel processing of 96 CUT&Tag samples in a standard microplate. Plate-CUT&Tag can be carried out in a similar time frame to benchtop CUT&Tag and yields data of comparable quality. We present data from cell culture and patient leukemia samples processed with Plate-CUT&Tag to illustrate its utility in large-scale preclinical and translational studies.

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Johnson, B. B., Boyle, G. E., Federico, A. J., Ma, J., Hemani, H., Spencer, D. H., Sarthy, J. F., Meers, M. P.. 2025-09-20. A protocol for high-throughput microplate-based CUT&Tag. https://doi.org/10.1101/2025.09.18.676951

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