Data

Source of data.

These examples assume that the data has been loaded, preprocessed (e.g. QC-ed, UMAP) and annotated (e.g. sample names, cell types, cell niches). For information, the preprocessing applied here is included in data preparation below. Please note that these are not full annotations, and do not aim to reproduce the authors’ published analyses! These are simplified and rough annotations to enable running these tests.

• Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease from Garrido-Trigo et al 2023.(Garrido-Trigo et al. 2023) : This dataset includes cosmx samples across 9 individuals; 3 healthy, 3 with chrones disease and 3 with Ulcerative colitis.
  • IBD cosmx dataset Seurat : As a seurat object
  • IBD cosmx dataset SFE : As a bioconductor SpatialFeatureExperiment object
• Alzheimers Plaques cosmx: Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer’s disease mouse model, as revealed by spatial transcriptomics (Mallach et al. 2024)
• Wnt4 KO in developing mouse kidney - 10X Chromium scRNAseq: Forming nephrons promote nephron progenitor maintenance and branching morphogenesis via paracrine BMP4 signalling under the control of Wnt4 (Moreau et al. 2023) : This dataset has 4 pools of single cell RNAseq data, total and conditional Wnt4 knockouts in E14.5 mouse kidney.

References

Garrido-Trigo, Alba, Ana M. Corraliza, Marisol Veny, Isabella Dotti, Elisa Melón-Ardanaz, Aina Rill, Helena L. Crowell, et al. 2023. “Macrophage and Neutrophil Heterogeneity at Single-Cell Spatial Resolution in Human Inflammatory Bowel Disease.” Nature Communications 14 (1): 4506. https://doi.org/10.1038/s41467-023-40156-6.

Mallach, Anna, Magdalena Zielonka, Veerle van Lieshout, Yanru An, Jia Hui Khoo, Marisa Vanheusden, Wei-Ting Chen, et al. 2024. “Microglia-Astrocyte Crosstalk in the Amyloid Plaque Niche of an Alzheimer’s Disease Mouse Model, as Revealed by Spatial Transcriptomics.” Cell Reports 43 (6): 114216. https://doi.org/10.1016/j.celrep.2024.114216.

Moreau, Julie L. M., Sarah Williams, Jihane Homman-Ludiye, Andrew J. Mallett, and Alexander N. Combes. 2023. “Forming Nephrons Promote Nephron Progenitor Maintenance and Branching Morphogenesis via Paracrine BMP4 Signalling Under the Control of Wnt4.” https://doi.org/10.1101/2023.11.19.567482.