Maternal Cell Transfer via Milk: Single-Cell RNA-seq Analysis

This repository contains the analysis code and documentation for single-cell RNA-seq analysis of maternal cells transferred through milk to nursing pups.

Overview

This project analyzes single-cell RNA-seq data from mouse pup blood samples to identify and characterize maternal cells transferred via nursing. Using GFP-labeled maternal cells, we track and analyze transferred immune cells in the offspring circulation, focusing on macrophage populations and their transcriptional signatures.

Repository Contents

• make_figures.qmd: Main analysis workflow in Quarto format
  • Quality control and filtering
  • Cell type annotation
  • Differential expression analysis
  • Pathway enrichment analysis
  • Publication-quality figure generation

Key Findings

• Identification of maternal cells transferred via milk in nursing pup blood
• Characterization of transferred macrophage populations
• Differential gene expression and pathway analysis of maternal vs. control cells
• Evidence of maternal immune cell transfer through lactation

Analysis Workflow

1. Data Loading: Process 10X Genomics single-cell data
2. Quality Control: Filter cells based on QC metrics
3. Doublet Detection: Remove doublets using scDblFinder
4. Normalization: Log-normalize and scale data
5. Dimensionality Reduction: PCA and UMAP
6. Cell Type Annotation: Manual and automated (SingleR) annotation
7. Differential Expression: Compare GFP+ vs control macrophages
8. Pathway Analysis: Enrichment analysis using MSigDB gene sets

Requirements

R Packages

• Seurat
• SingleR
• tidyverse
• dittoSeq
• ggrepel
• scDblFinder
• mascarade
• msigdbr
• UCell
• patchwork

Usage

To reproduce the analysis:

# Open and render the Quarto document
quarto::quarto_render("make_figures.qmd")

Output

The analysis generates publication-ready figures including:

• UMAP visualizations by sample origin and cell type
• Volcano plots for differential expression
• Pathway enrichment heatmaps
• Dotplots for marker gene expression

Contact

For questions about this analysis, please open an issue in this repository.

License

This project is licensed under the MIT License.