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Comparison and critical assessment of single-cell Hi-C protocols. / Gridina, M.; Taskina, A.; Lagunov, T. et al.

In: Heliyon, Vol. 8, No. 10, e11023, 10.2022.

Research output: Contribution to journal › Article › peer-review

Harvard

Gridina, M, Taskina, A, Lagunov, T, Nurislamov, A, Kulikova, T, Krasikova, A & Fishman, V 2022, 'Comparison and critical assessment of single-cell Hi-C protocols', Heliyon, vol. 8, no. 10, e11023. https://doi.org/10.1016/j.heliyon.2022.e11023

APA

Gridina, M., Taskina, A., Lagunov, T., Nurislamov, A., Kulikova, T., Krasikova, A., & Fishman, V. (2022). Comparison and critical assessment of single-cell Hi-C protocols. Heliyon, 8(10), [e11023]. https://doi.org/10.1016/j.heliyon.2022.e11023

Vancouver

Gridina M, Taskina A, Lagunov T, Nurislamov A, Kulikova T, Krasikova A et al. Comparison and critical assessment of single-cell Hi-C protocols. Heliyon. 2022 Oct;8(10):e11023. doi: 10.1016/j.heliyon.2022.e11023

Author

Gridina, M. ; Taskina, A. ; Lagunov, T. et al. / Comparison and critical assessment of single-cell Hi-C protocols. In: Heliyon. 2022 ; Vol. 8, No. 10.

BibTeX

@article{fc08369d4dd74ce5bab028e38fe3edad,
title = "Comparison and critical assessment of single-cell Hi-C protocols",
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.",
keywords = "Chicken, Genome architecture, Oocyte, Single-cell Hi-C",
author = "M. Gridina and A. Taskina and T. Lagunov and A. Nurislamov and T. Kulikova and A. Krasikova and V. Fishman",
note = "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: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = oct,
doi = "10.1016/j.heliyon.2022.e11023",
language = "English",
volume = "8",
journal = "Heliyon",
issn = "2405-8440",
publisher = "Elsevier",
number = "10",

}

RIS

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 -

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