Protocol to retrieve unknown flanking DNA sequences using semi-site-specific PCR-based genome walking
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Updated: Jul 4, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
Hong Chen1, Cheng Wei1, Zhiyu Lin2
1State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, P.R. China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, P.R. China.
Abstract:
Here, we describe a protocol based on semi-site-specific primer PCR (3SP-PCR) to access unknown flanking DNA sequences. We specify the guidelines for designing primers for 3SP-PCR. We also describe experimental procedures for the 3SP-PCR, along with PCR product purification and subsequent sequencing and analysis. For complete details on the use and execution of this protocol, please refer to Wei et al.1.
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