scRNAseq-Gut-IFNB-IFNL

Ileum and Colon organoids were derived from small intestine biopsies from the same patient (i.e. same genetic background). The organoids were then treated with either IFN-B or IFN-L or both followed by single-cell RNA sequencing.

Experimental design

Scripts

• src/01_makeAnnotation.R - Scripts for generating the file annotations
• src/02_kallistoAlignment.sh - Bash script to run multiple kallisto alignments using file 02_runKB
• src/02_runKB.sh - Bash script to run kallisto|bustools on the scRNAseq data
• src/03_seuratPreProcess.R - Script to perform standard filtering of scRNAseq data
• src/04_techReplicateMerged.R - Script to merge technical replicates
• src/05_global_analysis_ISG_response.R - Scripts to analyse global expression of ISG's, treating the scRNAseq data as pseudo bulk
• src/06_seuratTreatmentSeparateAnalysis.R - Standard Seurat workflow and Label transfer for individual samples
• src/06_seuratTreatmentSeparateAnalysis_onlyISGs.R - Standard Seurat workflow subsetting for only ISGs
• src/07_seuratIntegratedAnalysis.R - Standard Seurat workflow and Label transfer on integrated samples
• src/08_CellChat.R - Script for analysing cell-cell communication
• src/modifiedDotPlot.R - My own modified version of DotPlot, that I use in some situations.