Atopic dermatitis in time and space

This repo documents the reproducible data analysis pipelines for AD in time and space project.

Data analysis pipeline

Check GitHub repo for any update.

View publication in Journal of Investigative Dermatology: Assessment of Spatial and Temporal Variation in the Skin Transcriptome of Atopic Dermatitis by Use of Minimally Invasive Punch Biopsies)

rmd	description
1-transcriptome-data-cleaning.Rmd	Data cleaning and curation
2-geo-upload.Rmd	Upload data to GEO
3-table1-tableS1.Rmd	Table 1 (Baseline characteristics) and Table S1 (sample metadata, subject metadata)
4-tableS2.Rmd	Table S2 (differential gene expression analysis)
5-figure1.Rmd	Figure 1 (PCA, heatmap, Venn)
6-figure2.Rmd	Figure 2 (Across-study functional enrichment analysis)
7-figure3.Rmd	Figure 3 (Variance partition analysis)
8-figure4.Rmd	Figure 4 (Space variation)
9-figureS1.Rmd	Figure S1 (Transcriptome heatmap, cosine distance)
10-figureS2.Rmd	Figure S2 (Genome regulatory elements)
11-figureS3.Rmd	Figure S3 (Time variation)
12-figureS4.Rmd	Figure S4 (Intraindividual variation)
13-figureS5.Rmd	Figure S5 (Time fluctuation of disease severity)
14-figureS6.Rmd	Figure S6 (Correlation heatmap of IL34, IL37, UGT3A2 and inflammatory biomarkers)

Shiny application for data exploration and downloading

• Shiny app

• Github

Data availability

• RNA-seq data is available at GEO under the accession number GSE193309