Single-nucleus RNA-Seq of Hepatoblastoma Tumors
Summary
This project explores the single-nucleus transcriptomic landscape of hepatoblastoma tumors and matched PDX models. Using Seurat and Harmony, I performed batch correction, dimensionality reduction, unsupervised clustering, and detailed cell type annotation to dissect tumor heterogeneity and the tumor microenvironment.
Project Highlights
- Built a fully Dockerized snRNA-seq workflow using Seurat and Harmony for batch correction and UMAP projection.
- Annotated over 10 cell clusters using marker gene signatures and GeneCards cross-referencing.
- Identified tumor subtypes and key microenvironmental compartments including stromal and immune cells.
- Performed differential expression analysis between tumor and PDX nuclei within fetal-like clusters, highlighting immune activation and stress pathways.