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Updated: Aug 5, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Protocol for haplotype-resolved genome comparison and allele-specific expression analysis across multiple tissues and
1Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, Shandong 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China.
None:
Haplotype-resolved genome comparison and allele-specific expression (ASE) analysis are essential for understanding how genomic diversity drives phenotypic variation. However, performing these analyses reproducibly across multiple tissues and individuals remains challenging. Here, we present a protocol for haplotype-resolved genome comparison and ASE analysis, extended to enable ASE profiling across multiple tissues and individuals. We describe steps for identifying and comparing haplotype-divergent sequences and alleles. We then detail procedures for detecting variants from RNA sequencing (RNA-seq) data and identifying ASE genes. For complete details on the use and execution of this protocol, please refer to Liu et al.1.
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