etbf_fbr_stromal_bulkseq
Bulk RNAseq analysis of stromal cells from peri-implant fibrosis of mice with and without ETBF infection
Science Score: 75.0%
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Bulk RNAseq analysis of stromal cells from peri-implant fibrosis of mice with and without ETBF infection
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Metadata Files
README.md
ETBF infection alters stromal cell gene expression in implant fibrosis
This repository contains processed data and code supporting the publication Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant.
Overview
This repository provides the bash and R scripts used to process and analyze the bulk RNA sequencing data used in the study, which investigates the role of ETBF infection on the transcriptomic profile of stromal cells surrounding a biomaterial (polycaprolactone, PCL) implant.
The raw data and aligned counts files have been deposited in NCBI's Gene Expression Omnibus (Edgar et al., 2002) and are accessible through GEO Series accession number GSE293564, containing RNA sequencing data from mice 6 weeks after a volumetric muscle loss injury and implantation of a synthetic biomaterial, with and without ETBF infection (n = 4, each group). On Day -11, both groups were treated with antibiotics. On Day -7, antibiotics were removed, the control group was inoculated with DPBS and the experimental group was inoculated with ETBF. On day 0, both groups underwent volumetric muscle loss surgery with PCL implantation in the defect space. Data was collected 6 week after implantation. Stromal (singlet, live, CD31-/CD45-, CD29+) cells were sorted from the harvested quadriceps and subsequently underwent bulk RNA sequencing.
Repository Contents
The aligned counts files are available in the data directory of this repository, and the results of this analysis are included in the results directory. All scripts required for the analysis are included in the scripts directory. This project used the renv package to ensure a reproducible environment, which can be used as:
r
install.packages("renv")
renv::restore()
The analysis scripts have been numbered in the appropriate order for use:
r
source("scripts/utils.R")
source("scripts/1_processing.R")
source("scripts/2_dge.R")
source("scripts/3_gsea.R")
Results and Figures
These scripts generate data used in the manuscript figures:
- Figure 3B is a volcano plot created from 2ETBFposvneg_dge.csv
- Figure 3C contains manually selected genes based on function, subsetted from 2ETBFposvneg_dge.csv
- Figure 3D reflects the results of 3reactomegsea.csv
- Figure S10 contains a miscellaneous category of significantly differentially expressed genes from 2ETBFposvneg_dge.csv
Figures were created using these exported results.
Citation
If you use this data or code, please cite our publication:
Yang, B. et al. Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant. Proceedings of the National Academy of Sciences 122, e2422169122 (2025).
Contact
For questions, comments, or concerns, please contact Kavita Krishnan at kkrishnan@jhmi.edu or open an issue in this repository.
Owner
- Name: Elisseeff Lab
- Login: Elisseeff-Lab
- Kind: organization
- Website: https://elisseefflab.jhu.edu/
- Repositories: 2
- Profile: https://github.com/Elisseeff-Lab
Citation (CITATION.cff)
preferred-citation:
type: article
message: "If you use our data or code, please cite our publication."
authors:
- family-names: "Yang"
given-names: "Brenda"
title: "Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant"
abstract: "The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response and fibrosis is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via infection with the pathogenic bacterial species enterotoxigenic Bacteroides fragilis (ETBF) and implanted particulate material (mean particle size <600 μm) of the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation, increased levels of neutrophils in lymphoid tissues, and altered skeletal muscle gene expression. At the PCL implant site, we found significant changes in the transcriptome of sorted stromal cells between infected and control mice, including differences related to ECM components such as proteoglycans and glycosaminoglycans. However, we did not observe ETBF-induced differences in fibrosis levels. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant."
doi: 10.1073/pnas.2422169122
date-released: 2025-05-12
url: "https://www.pnas.org/doi/abs/10.1073/pnas.2422169122"
journal: "Proceedings of the National Academy of Sciences"
pages: e2422169122
issue: 20
volume: 122
year: 2025
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