4 Example Experiment
Background (Workshop) 15 mins (aim to reduce)
- E.g. one of the cosmx studies from https://swbioinf.github.io/spatialsnippets/index_data.html
- Likely need to subsample the data?
- This is what the data is
- Replicate key analyses and plots, explaining the “why we do X instead of Y” throughout.
Notes
- If we reproduce something it’ll be figure 1d UMAP with celltypes, and maybe the celltype proportions (if time permits.). Maybe Figure 1b simplified - a heatmap of marker genes.
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Today’s workshop will use data from paper Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease (Garrido-Trigo et al. 2023).
Their study explored macrophage and neutorphil subtypes and localisation across immflammatory bowel disease using a combination of single cell RNAseq (10X), spatial RNAseq (cosmx). The authors have made their raw and annotated data available (and their code). There is also a browseable interface here: https://servidor2-ciberehd.upc.es/external/garrido/app/
The study included 9 cosmx slides of colonic biopsies
- 3x HC - Healthy controls
- 3x UC - Ulcerative colitis
- 3x CD - Chrones’s disease
We will do some basic processing of those 9 samples - QC, clustering and visualisation.