Whelan-scRNA-Esophagus-Dec21

This repository contain R scripts used for the Whelan Lab publication on the single-cell biology of the murine epithelium. Please download the 10X FASTQ files or the processed .txt matrices from the GEO accession []. Alternatively, feel free to use the Seurat R object aging.epi.Robj, also provided in the GEO accession.

The core dependencies for these scripts:

1. R 4.0 https://www.r-project.org/

2. Seurat 4.0 https://satijalab.org/seurat/

3. Monocle 3 https://cole-trapnell-lab.github.io/monocle3/

For the supplementary verification of epithelial vs. stromal expression in our single-cell dataset, the following are also necessary:

4. Rsubread 2.8 https://bioconductor.org/packages/release/bioc/html/Rsubread.html

5. DESeq2 1.34 https://bioconductor.org/packages/release/bioc/html/DESeq2.html

For the main topics of our publication, the following pipeline of scripts was followed to create the files and figures discussed:

1. PreProcess_And_Cluster details the creation of the Seurat object, integration pipeline, and exclusion of non-epithelial cells in our dataset.

2. Epithelial_Figures delves further into the epithelial dataset and performs the analyses discussed in the paper.

3. Pseudotime_Monocle3 shows the process of trajectory inference as well as gene module calculation using Monocle 3.

The two imputation scripts show the process of label transfer and statistical analyses done on the imputation of each imputation comparison done in the paper. Finally, Epithelium_VS_Stroma processes the FASTQ files of epithelial and stromal samples to determine DEGs enriched in the epithelium.