Single-cell Gene Regulatory Network analysis with SCENIC+ at three timepoints of the DSS-induced colitis mouse model

This repository contains the processed single-cell RNA/ATAC objects and the Gene Regulatory Network (GRN) SCENIC+ analysis on fibroblasts of the mouse colon during homeostasis, acute inflammation and active regeneration of the acute DSS colitis mouse model. All files are associated with the analyses described in our manuscript with title: Distinct enhancer-driven transcriptional networks shape intestinal fibroblast identities and regeneration-associated activation In-house raw data from this work are deposited in GEO with the following accession numbers: scRNA-seq - Control colon (Healthy): GSE296873 - Regenerating colon (Regeneration): GSE304016 - Acute inflammation (InflammationK) and control (HealthyK), from Kinchen et al (https://doi.org/10.1016/j.cell.2018.08.067): GSE114374 scATAC-seq - Homeostasis, acute inflammation and regeneration: GSE304192 The code associated with this work is deposited in github: https://github.com/AthanasiaSt/SCENICPLUS-at-three-timepoints-of-the-DSS-induced-colitis-mouse-model.git Contents scRNA-seq - Seurat5_Harmony_integration_all_samples_Healthy_Inflammation_Regeneration_fibroblasts.rds – Seurat object containing the expression profiles of the four samples Healthy, HealthyK, InflammationK, Regeneration scATAC-seq - Final_ArchR_object/ - ArchR output folder with Healthy, Inflammation, Regeneration fibroblasts analysis including filtered and annotatted cells. Available matrices:"GeneIntegrationMatrix", "GeneScoreMatrix", "MotifMatrix", "PeakMatrix", "TileMatrix". It can be loaded with ArchR's function `loadArchRProject()`. ArchR's full manual: https://www.archrproject.com/bookdown/index.html SCENIC+ Results - Scenicplus_output.h5mu – The main output of the pipeline as a MuData file- eRegulon_direct.tsv – The inferred direct enhancer-driven regulons - Direct_Positive_eRegulons_filtered_basedOn_GeneBased_AUC.csv – Filtered positive regulons used in our analysis ------------------------------------------------------------------------ Methods Summary Preprocessing - Raw scRNA FASTQ files were processed using 10X Genomics CellRanger v7.1.0 (cellranger count, default parameters)- Raw scRNA FASTQ files from Kinchen dataset were downloaded and processed using 10X Genomics CellRanger v7.1.0 (cellranger aggr, default parameters including sequencing depth normalization)- Raw scATAC FASTQ files were processed using 10X Genomics CellRanger ATAC v2.1.0 (cellranger-atac count, default parameters)- Mouse reference transcriptome: mm10 Downstream Analysis - scRNA-seq QC, Harmony integration (In-house/Kinchen), clustering, plotting: Seurat v5.1.0- scATAC-seq QC, clustering, plotting, peaks, motifs: ArchR v1.0.2- Gene Regulatory Network inference: SCENIC+ v1.0a1 For more details on our methodology, see our manuscript and our GitHub repository: https://github.com/AthanasiaSt/SCENICPLUS-at-three-timepoints-of-the-DSS-induced-colitis-mouse-model.git------------------------------------------------------------------------ Citation If you use this dataset, please cite the associated manuscript:........... ------------------------------------------------------------------------ Contact For questions or data issues, please contact: Athanasia StavropoulouB.S.R.C "Alexander Fleming"