Part 1: Addressing feedback for study, input data, qc sections

20-study.Rmd

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+# Study overview
+
+## Learning objectives
+
+- Explain why spatial transcriptomics is used to study immune cell organisation
+in IBD  
+- Describe how the data set is structured with healthy and disease cohorts
+- Evaluate how replicates and balanced sampling improves the reliability of
+spatial transcriptomic studies
+
+## Background
+
+This workshop will use CosMx Spatial Molecular Imager (SMI) data from the paper
+_Macrophage and neutrophil heterogeneity
+at single-cell spatial resolution in human inflammatory bowel disease_
+(Garrido-Trigo et al. 2023)[^1].
+
+[^1]: https://doi.org/10.1038/s41467-023-40156-6
+
+This data set was chosen because the authors have made their raw and
+annotated data available, along with the corresponding analysis
+[code](https://github.com/HelenaLC/CosMx-SMI-IBD) and a browsable
+[data interface](https://servidor2-ciberehd.upc.es/external/garrido/app/).
+
+The study provides a clear biological contrast between health and disease
+states. This disease cohort consists of donors with active **inflammatory bowel
+disease (IBD)**, a chronic inflammatory condition of the gastrointestinal (GI) tract,
+where **immune cell organisation within the tissue plays a central role in
+disease pathogenesis.**
+
+**Inflammatory bowel disease (IBD) is an umbrella term** that includes two main GI tract disorders with different characteristics: **Crohn's disease (CD)** and **ulcerative colitis (UC)**.
+
+Spatial transcriptomic technologies enable gene expression to be measured at
+subcellular resolution while preserving the tissue architecture, allowing
+researchers to uncover spatial patterns and cell-cell interactions that would be
+lost in conventional bulk or single-cell RNA-seq data. 
+
+## The experimental design and cohorts
+
+```{r echo=F,fig.align='center',out.width='90%'}
+knitr::include_graphics(
+  here::here("images/garrido-trigo_fig1a.png")
+)
+```
+
+_Fig 1a from Garrido-Trigo et al. (2023)._
+
+The study included 9 CosMx slides of colonic biopsies, from a total of 9 donors:
+
+| Cohorts                | Abbreviated | Number of samples |
+| ---------------------- | ----------- | ----------------- |
+| **Healthy controls**   | HC          | 3                 |
+| Ulcerative colitis     | UC          | 3                 |
+| **Crohn's disease**    | CD          | 3                 |
+
+The study includes **three biological replicates per condition** (HC, UC, CD).
+This **provides enough variation to capture differences between individuals** while
+maintaining manageable data size for hands-on analysis.
+
+In this workshop, we will focus on the **healthy control (HC)**
+and **Crohn's disease (CD)** samples.
+
+In the original paper, the CosMX SMI cells were annotated via label transfer from
+the scRNA data. The spatial transcriptomics data will be processed independent of the scRNA data to demonstrate how differences in cellular composition and spatial organisation can be inferred directly from the spatial CosMx data.
+
+TODO: Include image of plots that will be created in downstream steps.