Standard

An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries. / Kechin, Andrey; Boldyreva, Darya; Borobova, Viktoriya и др.

в: Journal of biochemistry, Том 170, № 5, 01.11.2021, стр. 675-681.

Результаты исследований: Научные публикации в периодических изданияхстатьяРецензирование

Harvard

Kechin, A, Boldyreva, D, Borobova, V, Boyarskikh, U, Scherbak, S, Apalko, S, Makarova, M, Mosyakin, N, Kaftyreva, L & Filipenko, M 2021, 'An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries', Journal of biochemistry, Том. 170, № 5, стр. 675-681. https://doi.org/10.1093/jb/mvab089

APA

Kechin, A., Boldyreva, D., Borobova, V., Boyarskikh, U., Scherbak, S., Apalko, S., Makarova, M., Mosyakin, N., Kaftyreva, L., & Filipenko, M. (2021). An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries. Journal of biochemistry, 170(5), 675-681. https://doi.org/10.1093/jb/mvab089

Vancouver

Kechin A, Boldyreva D, Borobova V, Boyarskikh U, Scherbak S, Apalko S и др. An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries. Journal of biochemistry. 2021 нояб. 1;170(5):675-681. doi: 10.1093/jb/mvab089

Author

Kechin, Andrey ; Boldyreva, Darya ; Borobova, Viktoriya и др. / An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries. в: Journal of biochemistry. 2021 ; Том 170, № 5. стр. 675-681.

BibTeX

@article{748e1a4ca3cb459c8bd81d819cf13a0c,
title = "An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries",
abstract = "Next-generation sequencing (NGS)-library preparation for whole-genome sequencing (WGS) starts with DNA fragmentation, and sonication is a physical approach used most often due to its simplicity and reproducibility. However, the commercially available Covaris instrument has a high price for both the device and consumables. Here, we describe our in-house method of DNA shearing by sonication with small (100-600 µm) glass beads and an ultrasonic bath. The fragmentation conditions were optimized for the bacterial WGS with ∼550-bp fragment size (the ultrasonic bath water temperature 5-10°C, glass beads 0.06 g, the fragmentation time 50 s) and for human DNA with ∼250 bp (fragmentation with the same parameters for 4 min). Fragmentation results were compared with the Covaris instrument for preparing several bacterial NGS libraries for Illumina NGS platforms by several characteristics. We obtained close mean fragment lengths (523-623 versus 480-646), similar mono- and dinucleotide specificity of shearing, and comparable indicators of read alignment and de novo assembly for both methods. Thus, the described method is a new fast, and effective DNA fragmentation approach that can be used in different WGS applications.",
keywords = "DNA fragmentation, glass beads, shearing, sonication, whole-genome sequencing",
author = "Andrey Kechin and Darya Boldyreva and Viktoriya Borobova and Ulyana Boyarskikh and Sergey Scherbak and Svetlana Apalko and Maria Makarova and Nikolay Mosyakin and Lidia Kaftyreva and Maxim Filipenko",
note = "Publisher Copyright: {\textcopyright} 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.",
year = "2021",
month = nov,
day = "1",
doi = "10.1093/jb/mvab089",
language = "English",
volume = "170",
pages = "675--681",
journal = "Journal of biochemistry",
issn = "0021-924X",
publisher = "Oxford University Press",
number = "5",

}

RIS

TY - JOUR

T1 - An inexpensive, simple and effective method of genome DNA fragmentation for NGS libraries

AU - Kechin, Andrey

AU - Boldyreva, Darya

AU - Borobova, Viktoriya

AU - Boyarskikh, Ulyana

AU - Scherbak, Sergey

AU - Apalko, Svetlana

AU - Makarova, Maria

AU - Mosyakin, Nikolay

AU - Kaftyreva, Lidia

AU - Filipenko, Maxim

N1 - Publisher Copyright: © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

PY - 2021/11/1

Y1 - 2021/11/1

N2 - Next-generation sequencing (NGS)-library preparation for whole-genome sequencing (WGS) starts with DNA fragmentation, and sonication is a physical approach used most often due to its simplicity and reproducibility. However, the commercially available Covaris instrument has a high price for both the device and consumables. Here, we describe our in-house method of DNA shearing by sonication with small (100-600 µm) glass beads and an ultrasonic bath. The fragmentation conditions were optimized for the bacterial WGS with ∼550-bp fragment size (the ultrasonic bath water temperature 5-10°C, glass beads 0.06 g, the fragmentation time 50 s) and for human DNA with ∼250 bp (fragmentation with the same parameters for 4 min). Fragmentation results were compared with the Covaris instrument for preparing several bacterial NGS libraries for Illumina NGS platforms by several characteristics. We obtained close mean fragment lengths (523-623 versus 480-646), similar mono- and dinucleotide specificity of shearing, and comparable indicators of read alignment and de novo assembly for both methods. Thus, the described method is a new fast, and effective DNA fragmentation approach that can be used in different WGS applications.

AB - Next-generation sequencing (NGS)-library preparation for whole-genome sequencing (WGS) starts with DNA fragmentation, and sonication is a physical approach used most often due to its simplicity and reproducibility. However, the commercially available Covaris instrument has a high price for both the device and consumables. Here, we describe our in-house method of DNA shearing by sonication with small (100-600 µm) glass beads and an ultrasonic bath. The fragmentation conditions were optimized for the bacterial WGS with ∼550-bp fragment size (the ultrasonic bath water temperature 5-10°C, glass beads 0.06 g, the fragmentation time 50 s) and for human DNA with ∼250 bp (fragmentation with the same parameters for 4 min). Fragmentation results were compared with the Covaris instrument for preparing several bacterial NGS libraries for Illumina NGS platforms by several characteristics. We obtained close mean fragment lengths (523-623 versus 480-646), similar mono- and dinucleotide specificity of shearing, and comparable indicators of read alignment and de novo assembly for both methods. Thus, the described method is a new fast, and effective DNA fragmentation approach that can be used in different WGS applications.

KW - DNA fragmentation

KW - glass beads

KW - shearing

KW - sonication

KW - whole-genome sequencing

UR - http://www.scopus.com/inward/record.url?scp=85123226424&partnerID=8YFLogxK

UR - https://www.elibrary.ru/item.asp?id=47558877

U2 - 10.1093/jb/mvab089

DO - 10.1093/jb/mvab089

M3 - Article

C2 - 34382083

AN - SCOPUS:85123226424

VL - 170

SP - 675

EP - 681

JO - Journal of biochemistry

JF - Journal of biochemistry

SN - 0021-924X

IS - 5

ER -

ID: 35322134