Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data.

ABSTRACT: Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool for understanding gene function across diverse cells. Recently, this has included the use of allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level. We reasoned that because intronic reads are more prevalent in single-nucleus RNA-Seq (snRNA-Seq), and introns are under lower purifying selection and thus enriched for genetic variants, that snRNA-seq should facilitate single-cell analysis of ASE. Here we demonstrate how experimental and computational choices can improve the results of allelic imbalance analysis. We explore how experimental choices, such as RNA source, read length, sequencing depth, genotyping, etc., impact the power of ASE-ba

SUBMITTER: Simmons SK 

PROVIDER: S-EPMC11343128 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature