Data from: An autoinhibitory feedback mechanism preserves intestinal stem cell maintenance and fate commitment

This dataset contains the Seurat objects necessary to recreate all figures from the publication. The files included are as follows: Ctrl_NotchKO_integrated_scent: The primary integrated Seurat object containing Control and Notch KO samples. It includes the final high-resolution cell type annotations. RNAi_experiments_integrated: The integrated Seurat object containing all RNAi perturbation experiments (Control, Notch RNAi, CphUp and NotchRNAi+CphRNAi). It includes the final high-resolution cell type annotations. Ctrl_NotchKO_progenitors_integrated_meld: A subset of the Control/Notch KO dataset restricted specifically to progenitor populations (ISCs, EBs, and EEPs). It contains MELD likelihood scores used to quantify the probability of cells belonging to the perturbed condition. seuratKO_slingshot_object_integrated: A Seurat object containing trajectory inference results generated using Slingshot and Condiments. It includes specific dimensional reductions and lineage curves used to visualize the lineages. differential_expression_results.zip: Contains the differential gene expression results using either the pseudobulk with edgeR approach or Seurat FindMarkers function with test.use=“MAST“ . gene_sets.rds: contains the gene sets that were used to run GSEA and ORA. plotSmoothers_data.rds: Pre-computed smoothed expression data extracted from the tradeSeq GAM model for all genes. Contains fitted expression values along pseudotime trajectories for each lineage and condition, used to visualize gene expression dynamics along differentiation trajectories without re-computing the smoothers each time. tradeSeq_fit_condiments_strict.rds: A fitted tradeSeq generalized additive model (GAM) object for trajectory-based differential expression analysis. The model was fit with 6 knots on the Slingshot trajectory data, incorporating condition information (Control vs Notch KO) to enable testing for differential gene expression along pseudotime between conditions. tradeSeq_condition_test_res_strict.rds: Results from the tradeSeq conditionTest function, containing statistical test results for genes differentially expressed between Control and Notch KO conditions along each of the four lineages. Includes p-values and adjusted p-values (FDR) for identifying genes with condition-specific expression dynamics during differentiation. slingshot_individual_fit.rds: Condition-specific Slingshot trajectory objects fitted separately for Control and Notch KO using the conditments package.