DOI: 10.5281/zenodo.7780794
title: Single cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis

description: Codes and single cell data for "<strong>Single cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis</strong>" paper. <strong>File: Tunel_Lyve1_Data.xlsx </strong>– quantifications of Tunel+Lyve1+ cells for n=4 NECs and n=4 neonatal samples. <strong>Folder: Cell_ranger_output</strong> Data produced using 10x sequencing. This folder contains all the Cell Ranger output raw files from all 11 subjects used for single cell RNA sequencing (5x Neonatal- S1056, S1127, S1212, S1214, S1082, 6x NECs- S1021, S1074, S1095, S1109, S1155, S1193). The neonatal subjects had two 10X runs (except subject 1082) - one done on CD45 negatively selected small intestinal cells and the other on non-selected small intestinal cells. The NEC subjects had one run each (subject 1074 was sequenced twice) with no selection due to low yield in the selected runs. <strong>Folder: Seurat_pipeline</strong> 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. BG_subtraction_before_seurat.R - Script that creates a BG subtracted matrix for each CellRanger output before Seurat analysis. seurat_pipline_all_cells_NEC.R - Script for Seurat analysis for the full atlas. Final_seurat_obj_after_filtration_all_cells.rds – rds file of final Seurat object of all cells after pipeline filtration Files description in “RDS_files_for_seurat_pipeline” folder: list_UMIs_after_BG_subtruction.rds – rds file containing a list of all 10x runs used in the study after background subtraction. Used as input file for “seurat_pipline_all_cells_NEC.R” script. list_metadata_after_BG_subtruction.rds – rds file containing a list of metadata for all 10x runs used in the study after background subtraction. Used as input file for “seurat_pipline_all_cells_NEC.R” script. <strong>Folder: Deconvolution_analysis</strong> Done on Matlab R2019b This folder contains the script for deconvolution analysis and its input files. Deconvolution_parsing_NEC_for_zenodo.m - Matlab script to create box plots of deconvolution results and their q- values. Files description: deconvolution_original8_clusters.mat – structure of deconvolution results. Signature cells were split into the 8 major cell type groups shown in figure 1. cellanneal_split_clust_results.mat – structure of deconvolution results. Signature cells were split into sub groups for each cell type group. <strong>Folder: Ligand-receptor_interaction_analysis</strong> This folder contains matlab and R scripts for ligand-receptor interaction analysis. run_permutations_for_lig_rec_ratio_tensor_Zenodo.m – main script to run ligand-receptor analysis. calculate_ratio_ligand_receptor.m – function used by the main script. Interactions_visualizations_heatmaps.R – R script for heatmap visualization. Files description in “Mat_files_for_analysis” folder: all_cells_split_for_interactions.mat – single cell structure of all cells. Cells are split into subgroups for ligand receptor analysis. ramilowsky.mat – ligand-receptor lists taken from Ramilowski et al. 2015 to use in main script and function. tensor_real_q100permutations.mat – output mat file of the interactions ratio, q values and ligand-receptor names for heatmaps visualization in R (input file for “Interactions_visualizations_heatmaps.R”).