FemXpress: Systematic Analysis of X Chromosome Inactivation Heterogeneity in Female Single-Cell RNA-Seq Samples.

ABSTRACT: X chromosome inactivation (XCI) is crucial for balancing X-linked gene dosage in female cells by randomly silencing one X chromosome during early embryogenesis. However, accurately classifying cells based on the parental origin of the inactivated X chromosome in single-cell samples remains challenging. Here we present FemXpress, a computational tool leveraging X-linked single nucleotide polymorphisms (SNPs) to group cells based on the origin of the inactivated X chromosome in female single-cell RNA sequencing (scRNA-Seq) data. FemXpress performs robustly on both simulated and real datasets, without requiring parental genomic information, and can also identify genes that escape XCI. Applying FemXpress to single-cell RNA-Seq data from multiple tissues of a cynomolgus monkey, we reveal hetero

SUBMITTER: Wang X 

PROVIDER: S-EPMC12463006 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature