Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование
Comparison and critical assessment of single-cell Hi-C protocols. / Gridina, M.; Taskina, A.; Lagunov, T.; Nurislamov, A.; Kulikova, T.; Krasikova, A.; Fishman, V.
в: Heliyon, Том 8, № 10, e11023, 01.10.2022.Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование
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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 - Publisher Copyright: © 2022 The Author(s)
PY - 2022/10/1
Y1 - 2022/10/1
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
AN - SCOPUS:85140307451
VL - 8
JO - Heliyon
JF - Heliyon
SN - 2405-8440
IS - 10
M1 - e11023
ER -
ID: 99845518