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bioRxiv · 10.1101/2022.05.08.491066

Comparison and critical assessment of single-cell Hi-C protocols

Gridina, M.·Taskina, A.·Lagunov, T.·Nurislamov, A.·Kulikova, T.·Krasikova, A.·Fishman, V.
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Abstract

Advances in single-cell sequencing technologies make it possible to study the genome architecture in single cells. The rapid growth of the field has been fueled by the development of innovative single-cell Hi-C protocols. However, the protocols vary considerably in their efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. Here, we compare the two most commonly used single-cell Hi-C protocols. We use long-read sequencing to analyze molecular products of the Hi-C assay and show that whole-genome amplification step results in increased number of artifacts, larger coverage biases, and increased amount of noise compared to PCR-based amplification. Our comparison provides guidance for researchers studying chromatin architecture in individual cells.

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Gridina, M., Taskina, A., Lagunov, T., Nurislamov, A., Kulikova, T., Krasikova, A., Fishman, V.. 2022-06-01. Comparison and critical assessment of single-cell Hi-C protocols. https://doi.org/10.1101/2022.05.08.491066

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