Pollen Allergy SLIT Transcriptomics Project

This repository contains the analysis workflow for a multi-scale transcriptomics study of sublingual immunotherapy (SLIT) in pollen allergy.

Overview

The project integrates:

• Bulk RNA-seq analysis for GSE206149
• Single-cell RNA-seq / VDJ analysis for GSE200107
• A restart/helper script for the scRNA workflow
• A validation script using GSE206152

The analysis is organized into separate scripts and output folders so the workflow is easy to rerun and review.

Repository structure

.
├── Step1_GSE206149_bulk_rnaseq_focused_v6.R
├── Step2_GSE200107_scRNA_SLIT_pre_post_v1.R
├── Step3_GSE200107_merged_restart_and_helper.R
├── Step4_gse_206149_gse_206152_validation.r
├── figures/
├── results/
├── metadata/
├── plots/
└── README.md

What each script does

Step1_GSE206149_bulk_rnaseq_focused_v6.R
Processes bulk RNA-seq for GSE206149, runs differential expression and pathway analysis, and writes output tables and plots into project folders.

Step2_GSE200107_scRNA_SLIT_pre_post_v1.R
Processes the scRNA-seq / VDJ dataset, builds the Seurat object, performs clustering and annotation, and runs paired pseudobulk Post vs Pre SLIT analysis.

Step3_GSE200107_merged_restart_and_helper.R
Reloads the saved Seurat object, joins layers for Seurat v5 compatibility, regenerates markers, applies manual annotation, and reruns paired pseudobulk analysis.

Step4_gse_206149_gse_206152_validation.r
Validates the GSE206149 SLIT signature in GSE206152 by testing overlap, concordance, pathway consistency, and signature scoring.

Expected outputs

The scripts generate:

• metadata/ for parsed GEO metadata and sample mapping tables
• results/ for DE tables, summary tables, RDS files, and intermediate outputs
• plots/ for QC plots, volcano plots, heatmaps, and validation graphics
• figures/ for final report-ready panels

How to run

Run each script from the repository root so the relative paths resolve correctly:

source("Step1_GSE206149_bulk_rnaseq_focused_v6.R")
source("Step2_GSE200107_scRNA_SLIT_pre_post_v1.R")
source("Step3_GSE200107_merged_restart_and_helper.R")
source("Step4_gse_206149_gse_206152_validation.r")

Notes

• Large raw GEO downloads are not committed to the repository.
• Generated analysis artifacts can be kept if you want a fully reproducible archive, but consider excluding very large raw files.
• The figures in figures/ are the final report-ready panels.