Single cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis

Codes and single cell data for "Single cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis" paper.

File: Tunel_Lyve1_Data.xlsx – quantifications of Tunel+Lyve1+ cells for n=4 NECs and n=4 neonatal samples.

Folder: Cell_ranger_output

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.

Folder: Seurat_pipeline

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 CellRanger output before Seurat analysis.
2. seurat_pipline_all_cells_NEC.R - Script for Seurat analysis for the full atlas.
3. Final_seurat_obj_after_filtration_all_cells.rds – rds file of final Seurat object of all cells after pipeline filtration
4. Files description in “RDS_files_for_seurat_pipeline” folder:
   1. 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.
   2. 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.

Folder: Deconvolution_analysis

Done on Matlab R2019b

This folder contains the script for deconvolution analysis and its input files.

1. Deconvolution_parsing_NEC_for_zenodo.m - Matlab script to create box plots of deconvolution results and their q- values.
2. Files description:
   1. deconvolution_original8_clusters.mat – structure of deconvolution results. Signature cells were split into the 8 major cell type groups shown in figure 1.
   2. cellanneal_split_clust_results.mat – structure of deconvolution results. Signature cells were split into sub groups for each cell type group.

Folder: Ligand-receptor_interaction_analysis

This folder contains matlab and R scripts for ligand-receptor interaction analysis.

1. run_permutations_for_lig_rec_ratio_tensor_Zenodo.m – main script to run ligand-receptor analysis.
2. calculate_ratio_ligand_receptor.m – function used by the main script.
3. Interactions_visualizations_heatmaps.R – R script for heatmap visualization.
4. Files description in “Mat_files_for_analysis” folder:
   1. all_cells_split_for_interactions.mat – single cell structure of all cells. Cells are split into subgroups for ligand receptor analysis.
   2. ramilowsky.mat – ligand-receptor lists taken from Ramilowski et al. 2015 to use in main script and function.
   3. 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”).