TIME-RESOLVED MORPHOLOGICAL AND TRANSCRIPTOMIC CHARACTERIZATION OF EARLY ENTERIC NEURON SUBTYPE EMERGENCE IN CHICK

This repository contains the rds files generated and used in the article of André et al., 2026 The folder “Chick_E5E6E7” contains the main objects generated by our study (IntNCC_ENSb.rds and WholeGUT_annotated_simple.rds ) The folder “Chick_derived” includes additional objects used by the scripts that generated the figures. (ENS_5_rpca_2.rds, Chick/ENS_6_rpca_2.rds, ENS_7_2.rds, integration_sn_gut_harmonized_neuroblasts_neurons_subset.rds, Neuron_E5_rpca_b.rds, Neuron_E6_rpca_b.rds, Neuron_E7_b.rds, WholeGUT_annotated_DetailedENS_Cellchat.rds, WholeGUT_annotated_simple_ENS.rds). The “Public_datasets_reanalyzed” contains the human and mouse objects used to generate the figures ( elmentaite_6_11.rds,elmentaite_neuron_small_int_6_11_cluster_homemade_2_5_clean.rds, HumanNeu_2.rds, clust08RPCA_HumanNeu_conservedOrtho2508_One2OneOnly_26countNorm_final.rds, MousE12and14_IntMNN_NoDoublet22.rds, MouseMorarach_E15_logNres1_2.rds, ReclustNeu_IntMNN_MouseE12E14_Ortho2508L1One2One_CountandData_nom.Rds ). These objects utilize the data from Elmentaite et al., 2021 (1), Zhou et al., 2024 (2) and Morarach et al., 2021 (3) 1. R. Elmentaite, et al., Cells of the human intestinal tract mapped across space and time. Nature 597, 250–255 (2021). 2. B. Zhou, et al., Identification of signaling pathways that specify a subset of migrating enteric neural crest cells at the wavefront in mouse embryos. Dev Cell 59, 1689-1706.e8 (2024). 3. K. Morarach, et al., Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing. Nat Neurosci 24, 34–46 (2021).