spatial-24h

This is a spatial transcriptomics project led by Dr. Katharina Botterman. It includes 10x Genomics Visium data of cardiac tissue 24 h after ischemia/reperfusion injury or sham surgery, from wildtype mice.

Sequencing data

Sequencing data, including fastq files and count matrices will be available upon publication or request.

Analysis

To recreate the full analysis you can follow the steps below.

Libraries

The following transcriptomics-specific libraries were used:

• Seurat v4.0.1
• clusterProfiler v4.2.1
• enrichplot v1.14.1
• org.Mm.eg.db v3.14.0
• yulab.utils v0.0.4

They can be installed with the following commands:

# Seurat
remotes::install_version("Seurat", version = "4.0.1")

# clusterProfiler etc.
BiocManager::install("clusterProfiler")
BiocManager::install("enrichplot")
BiocManager::install("org.Mm.eg.db")
install.packages("yulab.utils")

Additionally, the following standard R libraries were used:

• dplyr
• ggplot2
• patchwork
• scales
• readr
• ggrepel
• rstudioapi
• shiny

Instructions

To reproduce the analysis, clone this repository and place the spaceranger outputs inside the project folder under a sub-folder titled data. i.e. spatial-24h/data/spaceranger

By starting your R session with the R project file, spatial-24h.Rproj, your working directory will be set to project folder, no matter the location on your machine. This will allow easy reading/writing of data/results using relative paths.

0-full-analysis.R will create all necessary directories and run the full analysis in the appropriate order. Each analysis step can also be run individually for better interactivity, starting from 1-clustering.R.

Examples

To-do

• Add abstract and author list at submission
• Make input data available at submission, i.e. gene signatures, cluster markers, reference maps, slide images and spaceranger outputs.