Spatial RNAseq and Proteomics of HuBMAP Pancreas

Overview This repository contains scripts and files related to the differential expression (DE) analysis of RNAseq and protein expression data generated from GeoMX DSP libraries from four donor pancreases.

Repository Structure

.
├── DE_by_region
│   ├── data
│   │   └── P1-P4.QC.v3.xlsx
│   ├── results
│   │   ├── By_Region_DE_Results_2024-10-23.xlsx
│   │   └── plots
│   │       ├── endothelial_Body_vs_Head_DE_plot_2024-10-23.png
│   │       ├── endothelial_Body_vs_Neck_DE_plot_2024-10-23.png
│   └── scripts
│       └── DE_Distance_function.R
├── DistanceToDuct
│   ├── data
│   │   └── DistanceToMainPancreaticDuct.csv
│   ├── results
│   │   └── CIBERSORT
│   └── scripts
│       └── CIBERSORT.R
├── HuBMAP_nPOD
│   └── data
├── Proteomics
│   └── data
└── README.md

Directory Breakdown:

• DE_by_region/
  Contains analyses of differential expression by pancreatic region (e.g., Body vs Head, Neck vs Tail).

  • data/: Input data used for the analyses.

    • P1-P4.QC.v3.xlsx: QC and data for four donors.

  • results/: Contains results and plots of the DE analysis.

    • By_Region_DE_Results_2024-10-23.xlsx: Output summarizing DE analysis.
    • plots/: Contains PNG plots for each analysis.

• DistanceToDuct/
  Contains analyses related to Does gene expression level change with increasing (or decreasing) distance fro m main pancreatic duct?

Data was subset to regions of inerest that included an islet and each enriched-cell-type target (AOI) was analyzed separately (endothelial cells, acinar and other cells, beta cells, and duct cells)

• data/: Input data for distance-based analyses.

  • DistanceToMainPancreaticDuct.csv: Data for pancreatic duct distances. Created by Sam Ewing.

• results/: DE results based on distance.

  • CIBERSORT/: Contains CIBERSORT results and heatmaps.

• Proteomics/
  Contains analyses of proteomics data.

  • data/: Contains raw and processed data.

• HuBMAP_nPOD/
  Additional HuBMAP and nPOD analyses, including raw counts.

Reproducibility

To reproduce the analysis:

1. Download Original Data: Contact for access to the original .xlsx files.
2. Run Scripts: Use the provided R scripts to process data and generate results.

Contact

For questions, please contact:

Heather Kates
Email: [email protected]

Acknowledgements

This research was supported by NIH NIDDK grant 1U54DK127823-01 Multi-omic 3D tissue maps for a Human BioMolecular Atlas.