Related Experiment Video
Updated: Oct 10, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
Protocol for mapping sister chromatid exchanges and structural variations using sci-L3-strand-seq
Shiyang He1, Peter Chovanec1, Yi Yin1
1Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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.
Related Concept Videos
Sanger Sequencing
Conservative Site-specific Recombination and Phase Variation
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Separation of Sister Chromatids
At the onset of anaphase, separase, a proteolytic enzyme, is...
