Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing

Osama Hidmi; Sara Oster; Diala Shatleh; Jonathan Monin; Rami I. Aqeilan

doi:10.1016/j.xpro.2024.103059

Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing

Osama Hidmi^*
, Sara Oster
, Diala Shatleh
, Jonathan Monin
, Rami I. Aqeilan^*

^*Corresponding author for this work

Department of Immunology and Cancer Research

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

2 Scopus citations

Abstract

Physiological double-stranded breaks (DSBs) are a major source of genomic instability. Here, we present a protocol for mapping physiological DSBs by in-suspension break labeling in situ and sequencing (sBLISS) in a single-nucleotide resolution. We describe steps for cell fixation, labeling of DSBs, DNA isolation followed by in vitro transcription (IVT), reverse transcription, and library preparation. sBLISS provides a map of DSBs over the genome and can be used to study the role of different factors in DSB formation. For complete details on the use and execution of this protocol, please refer to Hidmi et al.¹

Original language	English
Article number	103059
Journal	STAR Protocols
Volume	5
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2024.103059
State	Published - 21 Jun 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Bioinformatics
Cancer
Cell Biology
Cell culture
Genomics
Molecular Biology
Sequence analysis

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10.1016/j.xpro.2024.103059

Cite this

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abstract = "Physiological double-stranded breaks (DSBs) are a major source of genomic instability. Here, we present a protocol for mapping physiological DSBs by in-suspension break labeling in situ and sequencing (sBLISS) in a single-nucleotide resolution. We describe steps for cell fixation, labeling of DSBs, DNA isolation followed by in vitro transcription (IVT), reverse transcription, and library preparation. sBLISS provides a map of DSBs over the genome and can be used to study the role of different factors in DSB formation. For complete details on the use and execution of this protocol, please refer to Hidmi et al.1",

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AU - Hidmi, Osama

AU - Oster, Sara

AU - Shatleh, Diala

AU - Monin, Jonathan

AU - Aqeilan, Rami I.

PY - 2024/6/21

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AB - Physiological double-stranded breaks (DSBs) are a major source of genomic instability. Here, we present a protocol for mapping physiological DSBs by in-suspension break labeling in situ and sequencing (sBLISS) in a single-nucleotide resolution. We describe steps for cell fixation, labeling of DSBs, DNA isolation followed by in vitro transcription (IVT), reverse transcription, and library preparation. sBLISS provides a map of DSBs over the genome and can be used to study the role of different factors in DSB formation. For complete details on the use and execution of this protocol, please refer to Hidmi et al.1

KW - Bioinformatics

KW - Cancer

KW - Cell Biology

KW - Cell culture

KW - Genomics

KW - Molecular Biology

KW - Sequence analysis

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ER -

Protocol for mapping physiological DSBs using in-suspension break labeling in situ and sequencing

Abstract

Bibliographical note

UN SDGs

Keywords

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