Peer-reviewedCC BY-NC-NDSTAR protocols
Protocol for mapping sister chromatid exchanges and structural variations using sci-L3-strand-seq.
- 1Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA. Electronic address: [email protected].
- 2Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
- 3Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA. Electronic address: [email protected].
Abstract
Understanding spontaneous genome rearrangement requires mapping both error-free and mutational repair outcomes, particularly error-free sister chromatid exchanges (SCEs). Here, we present a sci-L3-Strand-seq protocol capturing SCEs across thousands of single cells from 12-16 independent samples in one experiment. We detail steps for cell labeling, sample banking, nucleosome depletion, in situ combinatorial barcoding, enrichment of BrdU-labeled cells, and nascent strand ablation. We then detail linear amplification, reverse transcription, and second-strand synthesis. Libraries are typically sequencing-ready within three days from frozen cells. For complete details on the use and execution of this protocol, please refer to Chovanec et al.¹.
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BibTeX
@article{he2026protocol,
title = {{Protocol for mapping sister chromatid exchanges and structural variations using sci-L3-strand-seq.}},
author = {Shiyang He and Peter Chovanec and Yi Yin},
journal = {STAR protocols},
year = {2026},
month = oct,
doi = {10.1016/j.xpro.2026.104892},
url = {https://europepmc.org/article/MED/42848518},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Protocol for mapping sister chromatid exchanges and structural variations using sci-L3-strand-seq.
AU - Shiyang He
AU - Peter Chovanec
AU - Yi Yin
PY - 2026
DA - 2026/10/07
JO - STAR protocols
DO - 10.1016/j.xpro.2026.104892
UR - https://europepmc.org/article/MED/42848518
AB - Understanding spontaneous genome rearrangement requires mapping both error-free and mutational repair outcomes, particularly error-free sister chromatid exchanges (SCEs). Here, we present a sci-L3-Strand-seq protocol capturing SCEs across thousands of single cells from 12-16 independent samples in one experiment. We detail steps for cell labeling, sample banking, nucleosome depletion, in situ combinatorial barcoding, enrichment of BrdU-labeled cells, and nascent strand ablation. We then detail linear amplification, reverse transcription, and second-strand synthesis. Libraries are typically sequencing-ready within three days from frozen cells. For complete details on the use and execution of this protocol, please refer to Chovanec et al.¹.
SN - 2666-1667
ER -