RESEARCH DOSSIER · Single-cell & single-nucleus transcriptomics
Single-Cell Transcriptomics
SOX4 and Single-Cell & Single-Nucleus Transcriptomics
Investigating hepatobiliary cell populations and gene expression in cholestatic liver diseases using single-cell and single-nucleus sequencing.
Ongoing research
Research question
How can single-cell and single-nucleus transcriptomic analyses characterize SOX4 expression and hepatobiliary cell populations across cholestatic liver diseases?
Scientific background
My analytical work concerns SOX4 expression, cellular heterogeneity, and gene-expression regulation in liver biology. The scientific scope includes primary sclerosing cholangitis, primary biliary cholangitis, biliary atresia, and Alagille syndrome. These disease areas describe the scope of inquiry, not completed disease-specific findings.
Methods
My contribution centers on computational analysis of transcriptomic data and the assessment of cell populations and gene expression. Dataset-specific parameters, internal material, and unapproved results are withheld.
- Quality control, normalization, and highly variable gene identification for scRNA-seq and snRNA-seq
- PCA, dimensionality reduction, and UMAP
- Seurat analysis and Harmony integration
- Cell clustering, cell-type annotation, and marker-gene analysis
- Gene-expression and differential-expression analysis
Prospective approaches
- Pseudobulk analysis is a prospective approach; completed use is not established here.
Computational tools
Research progress & findings
Research analyses are ongoing. Detailed findings and unpublished results are not publicly available at this stage.
Figures & visualizations
No approved research figures are available for this dossier.
Interpretation
No disease-specific conclusions or mechanistic claims are presented here.
Limitations
Sampling, quality-control choices, batch effects, and cell-type annotation influence interpretation. Expression differences alone do not establish causal mechanisms; cells must not be treated as independent biological replicates when sample-level replication is required.
Current status
Research analyses are ongoing. Detailed findings and unpublished results are not publicly available at this stage.
Future directions
Continue quality assessment and analysis while keeping unpublished findings and collaborator information outside the public record.
Posters & research outputs
Ongoing research; detailed findings withheld