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Zenodo
2025
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| Online Access: | https://doi.org/10.5281/zenodo.17258163 |
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- <p>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 (Day 0), acute inflammation (Day 7) and active regeneration (Day 14), three timepoints of the acute DSS colitis mouse model.</p> <p>All files are associated with the analyses described in our manuscript with title: <strong>Distinct enhancer-driven transcriptional networks shape intestinal fibroblast identities and regeneration-associated activation</strong></p> <p>In-house raw data from this work are deposited in GEO with the following accession numbers: </p> <p><strong>scRNA-seq</strong><br> - Control colon (D0): GSE296873<br> - Regenerating colon (D14): GSE304016<br> - Acute inflammation (D7k) and control (D0k), from Kinchen et al (<a href="https://doi.org/10.1016/j.cell.2018.08.067">https://doi.org/10.1016/j.cell.2018.08.067</a>): GSE114374<br> <br><strong>scATAC-seq</strong><br> - Homeostasis (D0), acute inflammation (D7), regeneration (D14): GSE304192</p> <p><br>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</p> <p><strong>Contents</strong></p> <p><strong>scRNA-seq</strong></p> <p>- <em>Seurat5_Harmony_integration_all_samples_D0_D7_D14_fibroblasts.rds</em> – Seurat object containing the expression profiles of the four samples D0, D0k, D7, D14</p> <p><strong>scATAC-seq</strong></p> <p>- <em>Final_ArchR_object/</em> - ArchR output folder with D0, D7, D14 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 </p> <p><strong>SCENIC+ Results</strong></p> <p>- <em> Scenicplus_output.h5mu</em> – The main output of the pipeline as a MuData file<br>- <em>eRegulon_direct.tsv </em>– The inferred direct enhancer-driven regulons <br>- <em>Direct_Positive_eRegulons_filtered_basedOn_GeneBased_AUC.csv </em>– Filtered positive regulons used in our analysis</p> <p>------------------------------------------------------------------------</p> <p><strong>Methods Summary</strong></p> <p><strong>Preprocessing</strong></p> <p>- Raw scRNA FASTQ files were processed using 10X Genomics CellRanger v7.1.0 (<em>cellranger count</em>, default parameters)<br>- Raw scRNA FASTQ files from Kinchen dataset were downloaded and processed using 10X Genomics CellRanger v7.1.0 (<em>cellranger aggr</em>, default parameters including sequencing depth normalization)<br>- Raw scATAC FASTQ files were processed using 10X Genomics CellRanger ATAC v2.1.0 (<em>cellranger-atac count</em>, default parameters)<br>- Mouse reference transcriptome: mm10</p> <p><strong>Downstream Analysis</strong></p> <p>- scRNA-seq QC, Harmony integration (In-house/Kinchen), clustering, plotting: Seurat v5.1.0<br>- scATAC-seq QC, clustering, plotting, peaks, motifs: ArchR v1.0.2<br>- Gene Regulatory Network inference: SCENIC+ v1.0a1</p> <p>For more details on our methodology, see our manuscript .... and our GitHub repository: [link]<br>------------------------------------------------------------------------</p> <p><strong>Citation</strong></p> <p>If you use this dataset, please cite the associated manuscript:...........</p> <p> </p> <p>------------------------------------------------------------------------</p> <p><strong>Contact</strong></p> <p>For questions or data issues, please contact:</p> <p>Athanasia Stavropoulou<br>B.S.R.C "Alexander Fleming"</p>