Construction of Strand-seq libraries in open nanoliter arrays

Vincent C T Hanlon; Daniel D Chan; Zeid Hamadeh; Yanni Wang; Carl-Adam Mattsson; Diana C J Spierings; Robin J N Coope; Peter M Lansdorp

doi:10.1016/j.crmeth.2021.100150

Construction of Strand-seq libraries in open nanoliter arrays

Cell Rep Methods. 2022 Jan 24;2(1):100150. doi: 10.1016/j.crmeth.2021.100150.

Authors

Vincent C T Hanlon¹, Daniel D Chan¹, Zeid Hamadeh¹, Yanni Wang¹, Carl-Adam Mattsson¹, Diana C J Spierings², Robin J N Coope³, Peter M Lansdorp^{1

2

4}

Affiliations

¹ Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
² European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands.
³ Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
⁴ Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

Abstract

Single-cell Strand-seq generates directional genomic information to study DNA repair, assemble genomes, and map structural variation onto chromosome-length haplotypes. We report a nanoliter-volume, one-pot (OP) Strand-seq library preparation protocol in which reagents are added cumulatively, DNA purification steps are avoided, and enzymes are inactivated with a thermolabile protease. OP-Strand-seq libraries capture 10%-25% of the genome from a single-cell with reduced costs and increased throughput.

Keywords: Strand-seq; haplotyping; inversions; nanoliter dispensing; one-pot library construction; single-cell sequencing; structural genomic variation; thermolabile protease.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genomics* / methods
Haplotypes

Grants and funding

159787/CIHR/Canada