Insulin is expressed by enteroendocrine cells during human fetal development

Codes and single cell data for "Insulin is expressed by enteroendocrine cells during human fetal development" paper. Folder: Cell_Ranger_output Data produced using 10x sequencing. This folder contains all the Cell Ranger output raw files from all 6 subjects used for single cell RNA sequencing (2x Neonatal- S1056, S1127, 2x fetal 21 weeks GA- S1100A, S1102, 2x fetal 23weeks GA S1130, S1143). Each subject has two 10X runs- one done on CD45 negatively selected small intestinal cells and the other on non-selected small intestinal cells. Folder: Matlab_codes_and_struct Done on Matlab R2019b This folder contains two scripts and their input files. 1. Global_transcriptome_similarity_Matlab.m - Matlab script to create the distance from adult beta cells from Extended Data Fig 2 2. sturcture_for_global_similarity.mat - input file for "Global_transcriptome_similarity_Matlab.m" script 3. SCENIC_analysis_matlab.m - Matlab script to create clustergram of transcription factors with the most differential activities in the different cell types from Extended Data Fig 3 4. EECs_mat_file.mat - input file for "SCENIC_analysis_matlab.m" script Folder: Seurat_pipline_and_background_subtraction Done with Seurat package version 3.2.2 This folder contains R scripts for Seurat analysis and script for background (BG) subtraction of the data. 1. BG_subtraction_before_seurat.R - Script that creates a BG subtracted matrix for each Cell Ranger output before Seurat analysis. 2. seurat_pipline_all_cells.R - Script for Seurat analysis for the full atlas and the Enteroendocrine subset. Folder: Count_tables This folder contains three BG subtracted UMI tables and their additional metadata. 1. BG_subtracted_count_table_all_cells_before_filt.txt - BG subtracted UMI table of all cells before Seurat filtration and analysis (input file for "seurat_pipline_all_cells.R" script). 2. Metadata_all_cells_before_filteration.xlsx - Metadata for "BG_subtracted_count_table_all_cells_before_filt.txt " (input file for "seurat_pipline_all_cells.R" script). 3. BG_subtracted_count_table_all_cells_after_filt.txt - BG subtracted UMI table of all cells after Seurat filtration and analysis. 4. Metadata_all_cells_after_filteration.xlsx - Metadata for "BG_subtracted_count_table_all_cells_after_filt.txt". 5. BG_sub_count_table_enteroendocrine_cells.txt - BG subtracted UMI table of enteroendocrine cells subset after Seurat filtration and analysis. 6. Metadata_enteroendocrine_cells.xlsx - Metadata for "BG_sub_count_table_e