TY - JOUR

T1 - Comparison and critical assessment of single-cell Hi-C protocols

AU - Gridina, M.

AU - Taskina, A.

AU - Lagunov, T.

AU - Nurislamov, A.

AU - Kulikova, T.

AU - Krasikova, A.

AU - Fishman, V.

N1 - Funding Information: This work, including cells isolation and NGS library preparation, was supported by Russian Science Foundation grant #20-64-46021 . Illumina sequencing was performed by Skoltech Genomics Core Facility and BGI Sequencing Facilities. Long-read sequencing was performed using equipment of the Novosibirsk State University, supported by the Ministry of Education and Science of Russian Federation , grant #2019-0546 (FSUS-2020-0040). ONT data analysis was performed on the nodes of HPC cluster of the Institute of Cytology and Genetics, supported by the project No. 121031800061-7). Illumina data analysis was supported by strategic academic leadership program “Priority 2030” in Novosibirsk State University. Publisher Copyright: © 2022 The Author(s)

PY - 2022/10

Y1 - 2022/10

N2 - 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.

AB - 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.

KW - Chicken

KW - Genome architecture

KW - Oocyte

KW - Single-cell Hi-C

UR - http://www.scopus.com/inward/record.url?scp=85140307451&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/acb2bc85-2e5d-36ab-8e7f-82b294c8167e/

U2 - 10.1016/j.heliyon.2022.e11023

DO - 10.1016/j.heliyon.2022.e11023

M3 - Article

C2 - 36281413

AN - SCOPUS:85140307451

VL - 8

JO - Heliyon

JF - Heliyon

SN - 2405-8440

IS - 10

M1 - e11023

ER -