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bioRxiv · 10.1101/310284

High-throughput chromatin accessibility profiling at single-cell resolution

Mezger, A.·Klemm, S.·Mann, I.·Brower, K.·Mir, A.·Bostick, M.·Farmer, A.·Fordyce, P.·Linnarsson, S.·Greenleaf, W.
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Abstract

We have developed a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 hour on-chip processing time) and cost (~98{cents} per cell) compared to prior microfluidic implementations. We applied this method to measure regulatory variation in Peripheral Blood Mononuclear Cells (PBMCs) and show robust, de-novo clustering of single cells by hematopoietic cell type.

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Mezger, A., Klemm, S., Mann, I., Brower, K., Mir, A., Bostick, M., Farmer, A., Fordyce, P., Linnarsson, S., Greenleaf, W.. 2018-04-28. High-throughput chromatin accessibility profiling at single-cell resolution. https://doi.org/10.1101/310284

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