This repo will cover all of the code linked to Castillo R, Sidhu I et al.
(Manuscript Title: Spatial transcriptomics stratifies health and psoriatic disease severity by emergent cellular ecosystems )
All of the raw files linked to this project can be found under GEO Accession number - (GSE202011
GRAPHICAL DATA AND WORKFLOW OVERVIEW
Please make sure to install all of the dependencies prior to running the code. The following dependencies are essential:-
All of the processed data (Including RDS files) can be found at (https://doi.org/10.5281/zenodo.7562864 ).
CODE AND REPOSITORY NAVIGATION The code is organized into several R notebooks with each notebook covering different parts of the analysis. The figure numbers and references are found within each notebook and a table content will also be added to link each figure to different parts of the code for ease of navigation.
The notebooks will also require you to download the data from the linked Zenodo repository to reproduce all of the respective figures.
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
1B
link Spatial Plot - Healthy sample with cluster labels
1C
link UMAP (Healthy samples only) - with spatial regions labels
1D
link Percentage composition (Healthy samples only)
1E
link Seurat Integeration (scRNA + ST data) showing cell type enrichment
1G
link MIA - healthy skin with dataset 1 (Hughes et al.) - Structural cell types only
1H
link MIA - healthy skin with dataset 2 (Reynolds et al.) - Structural cell types only
1I
link MIA - healthy skin with dataset 3 (Sullivan et al.) - APCs and Preadiplocytes
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
2A
link MIA - healthy skin with dataset 1 (Hughes et al.) - Immune cell types only
2B
link MIA - healthy skin with dataset 2 (Reynolds et al.) - Immune cell types only
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
3A
link Spatial Plots with cluster labels - Lesional and Non-Lesional skin
3B
link UMAP - All samples combined (PS + Healthy skin) after Harmony batch correction
3C
link Percentage composition plots for different clusters / spatial regions
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
4E
link Circos plot visualization - cluster 4 receptor with clusters 7, 3 and 10 as ligand.
4F
link Circos plot visualization - cluster 7 receptor with clusters 10, 3 and 4 as ligand.
4G
link Circos plot visualization - cluster 10 receptor with clusters 7, 3 and 4 as ligand.
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
5A
link MIA for (PS only) dataset 1 - Immune cell types
5B
link MIA for (PS only) dataset 2 - Immune cell types
5C
link MIA for TRM (Tisssue resident memory cells) dataset
5D
link Space-fold projection - Healthy, non-lesional and lesional skin.
5E
link B cell (From dataset 1) pathways
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
6A
link Hierarchical clustering based heatmap for all samples
6B
link PCA plot for all samples - grouped by PS group
6C
link PCA plot for all samples - grouped by Disease severity
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
7A
link Space-fold projection - Mild disease (split into non-lesional and lesional)
7B
link Space-fold projection - Moderate-severe disease (split into non-lesional and lesional)
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
8A
link PCA plot - Pseudobulk for cluster 1 (Derm macrophages, fibroblasts)
8B
link PCA plot - Pseudobulk for cluster 12 (Derm macrophages, fibroblasts)
8E
link Spatial Feature plots #1
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S2-B
link Spatial Plots (Before and after filtering)
S2-C
link Heat-map showing top 8 marker genes per cluster (Healthy sample data only)
S2-D
link UMI counts
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S3-A
link Heatmap for Healthy samples - after Harmony batch correction
S3-B
link UMAP - Healthy skin after Harmony batch correction
S3-C
link Percentage composition plots for different clusters / spatial regions (Healthy skin)
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S4-A
link UMAP - healthy skin with scRNA dataset 1 (Hughes et al.)
S4-B
link UMAP - healthy skin with scRNA dataset 2 (Reynolds et al.)
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S5-A
link (Anchor data UMAP)UMAP plots - Harmony batch correction vs Anchor batch correction
S5-A
link (Harmony data UMAP)UMAP plots - Harmony batch correction vs Anchor batch correction
S5-C
link (Anchor data)Spatial plots- Harmony batch correction vs Anchor batch correction
S5-C
link (Harmony data)Spatial plots- Harmony batch correction vs Anchor batch correction
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S6
link Heat-map showing top 10 marker genes per cluster (All samples) - Harmony batch corrected
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S7
link Heat-map showing top 10 marker genes per cluster (All samples) - Anchor batch corrected
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S8-B
link UMIs per clusters - Harmony batch corrected data
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S9-A
link Seurat Integration (scRNA + ST data) showing cell type enrichment fpr psoriatic lesional skin ST
S9-B
link Psoriatic skin scRNA-seq dataset 1
S9-C
link Psoriatic skin scRNA-seq dataset 2
S9-D
link MIA - PS skin with dataset 1 (Hughes et al.) - Structural cell types only
S9-E
link MIA - PS skin with dataset 2 (Reynolds et al.) - Structural cell types only
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S10A
link Dendogram for all samples based on pseudo-bulk expression
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S11
link PCA plots - per cluster basis (PS samples only)
FIGURE NO
NOTEBOOK LINK
DESCRIPTION
S13
link Spatial Feature expression plots #2
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent