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Tutorial: TCM

This tutorial walks you through the T-Cell Map (TCM) module, showing you how to explore single-cell T-cell data.

Overview

The T-Cell Map module provides interactive visualization and analysis tools for single-cell T-cell RNA sequencing data. You can explore different T-cell populations, search for gene expression patterns, and analyze differential expression genes.

TCM Overview

Getting Started with TCM

1. Navigate to T-Cell Map

  1. Open reSCRP in your browser: https://scrp.breakthroughcancer.org
  2. Click on "TCM" in the navigation menu
  3. This opens the T-Cell Map visualization interface

2. Explore Cell Types

The main interface shows a UMAP plot with different T-cell populations:

TCM Embedding Visualization

Key features: - UMAP Plot: Interactive scatter plot showing cell clusters - Cell Type Legend: Identifies different T-cell populations - Color Coding: Each cell type has a distinct color

Available Cell Types: - CD4+ T cells - Helper T cells and their subsets - CD8+ T cells - Cytotoxic T cells and memory populations - Regulatory T cells (Tregs) - Immune suppressor cells - T Follicular Helper cells (TFH) - B cell helper populations - Proliferative cells - Actively dividing T cells - Innate-like cells - NK/MAIT cell populations

3. Search for Genes

Use the gene search functionality to explore expression patterns:

Example genes to try: 

CD4      # Helper T cell marker
CD8A     # Cytotoxic T cell marker
FOXP3    # Regulatory T cell marker
GZMB     # Cytotoxic granule marker
IL2      # Cytokine
IFNG     # Interferon gamma
TNF      # Tumor necrosis factor

How to search: 1. Enter a gene name in the search box 2. View expression levels across cell types 3. Observe spatial expression patterns on the UMAP 4. Compare expression between different conditions

4. Analyze Differential Expression Genes (DEGs)

Explore cluster-specific marker genes:

TCM DEGs Analysis

DEG Analysis Features: - Cluster-specific markers: Genes that define each cell type - Statistical significance: p-values and fold changes - Expression percentages: How many cells express each gene - Interactive tables: Sort and filter results

How to use DEGs: 1. Select a cell cluster of interest 2. View the top marker genes for that cluster 3. Click on genes to see their expression patterns 4. Export results for further analysis