Dataset for: "Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation"

This record contains the processed spatial transcriptomics datasets used in the manuscript
“Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation”.

The dataset includes unperturbed intestinal epithelial monolayers and sprinkling (cell
transplantation) experiments. Data are organized by experimental condition, timepoint (12 hr and
72 hr), and region of interest (ROI).

Each ROI directory contains:
- per-cell metadata (cell_attributes.csv),
- a cell-by-gene expression matrix (cell_by_gene.csv),
- corrected transcript tables used for spatial and zonation analyses
  (serial_genes_corrected.csv),
- and indices identifying normal epithelial cells included in the analysis
  (non_reg_cell_ind.csv).

A README.txt included in the archive describes the folder structure and file contents in detail.

IMPORTANT: This record does NOT include in vivo villus reference data published previously by
Moor et al., Cell (2018). Those data must be obtained directly from the original publication and
are used only for comparative analysis.

Code to reproduce all analyses and figures is available at:
https://github.com/nitzanlab/Resilience-of-spatial-structure-in-intestinal-organoids-revealed-by-spatial-transcriptomics