🧬 GBM_scRNAseq_KDM6B_Project

Reproducing Single-Cell RNA-seq Analysis of Glioblastoma Myeloid Cells

This repository documents a self-directed computational biology project aimed at reproducing key findings from:

Li et al.

Myeloid-specific KDM6B inhibition sensitizes glioblastoma to PD1 blockade.

using publicly available single-cell RNA sequencing data from GEO.

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Dataset

Resource	Information
GEO accession	GSE131928
Organism	Homo sapiens
Platform	10X Genomics
Sample analyzed	GSM3828673_10X_GBM_IDHwt_processed_TPM.tsv

Dataset:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131928

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Objectives

• Reproduce published findings from glioblastoma scRNA-seq data.
• Characterize myeloid populations.
• Investigate KDM6B expression heterogeneity.
• Perform clustering and marker analysis.
• Explore biological pathways and functional enrichment.

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Analysis Workflow

Data Import
      ↓
Seurat Object Construction
      ↓
Normalization
      ↓
Variable Feature Selection
      ↓
PCA
      ↓
Graph-based Clustering
      ↓
UMAP Visualization
      ↓
Marker Identification
      ↓
Myeloid Cell Extraction
      ↓
KDM6B Expression Analysis
      ↓
Figure Reproduction

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Software

• R (v4.5.3)
• RStudio
• Seurat v5
• DESeq2
• clusterProfiler
• ggplot2
• pheatmap

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Repository Structure

GBM_scRNAseq_KDM6B_Project
│
├── README.md
│
├── Scripts
│   ├── 01_data_import.R
│   ├── 02_seurat_pipeline.R
│   ├── 03_clustering_UMAP.R
│   ├── 04_marker_analysis.R
│   ├── 05_myeloid_subsetting.R
│   ├── 06_KDM6B_analysis.R
│   └── 07_figure_reproduction.R
│
├── Figures
├── Results
└── Environment

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Analyses Performed

✔ Data Import

• Loading processed expression matrix.

✔ Single-cell Analysis

• Seurat object construction
• Normalization
• Feature selection
• PCA
• UMAP

✔ Cell Clustering

• Graph-based clustering
• Marker gene identification

✔ Myeloid Cell Characterization

Using:

• CD68
• CD14
• CD163
• CX3CR1

✔ KDM6B Expression Analysis

• FeaturePlot
• Violin plot analysis

✔ Figure Reproduction

Attempted reproduction of key figures from:

Li et al.

Myeloid-specific KDM6B inhibition sensitizes glioblastoma to PD1 blockade.

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Skills Demonstrated

Bioinformatics

• Single-cell RNA-seq analysis
• Differential expression analysis
• Functional enrichment

Programming

• R
• Seurat
• Data visualization
• Reproducible workflows

Biological Interpretation

• Glioblastoma biology
• Tumor-associated macrophages
• Myeloid heterogeneity
• KDM6B signaling

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Future Directions

• Differential expression analysis
• GO enrichment
• Correlation analysis
• Figure 2 reproduction
• Integration with ChIP-seq data

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Author

Soumen Manna PhD Epigenetics | Cancer Biology