UTI HostOmics

Manuscript: Host endocrine-metabolic-immune remodeling across recurrent and pregnancy-associated uropathogenic Escherichia coli infection

• Version archive (v1.0.0): 10.5281/zenodo.21419897
• All-version concept DOI: 10.5281/zenodo.21419896
• Zenodo record: https://zenodo.org/records/21419897

This repository accompanies the study:

The study integrates four public transcriptomic resources to examine endocrine-metabolic-immune remodeling across urinary tract infection, recurrence-related bladder perturbation, pregnancy-associated outcomes, and cell-resolved UPEC host responses.

Biological scope

The analysis evaluates 78 curated submodules spanning:

• steroid, cholesterol, and endocrine signaling;
• lipid and adipokine biology;
• insulin receptor/IRS and PI3K-AKT signaling;
• inflammatory carbon, amino-acid, nucleotide, NAD, and redox metabolism;
• complement initiation, amplification, inflammatory, opsonophagocytic, and regulatory branches;
• immune-context and cell-state programs.

Public datasets

The source accessions are GSE112098, GSE186800, GSE252321, and GSE280297. Raw data are not redistributed. See data/accessions.tsv.

Repository structure

• config/modules/: curated biological module definitions.
• data/: public accession and acquisition documentation.
• environment/: software and runtime manifests.
• figures/main/: assembled main-figure TIFF files.
• manuscript/: journal-targeted working manuscript.
• references/: reference-management exports and supporting files.
• results/: selected final metadata, reports, and source-value tables.
• scripts/archive_phase_scripts/: phase-resolved computational provenance.
• supplemental/: supplemental workbook and legends.
• docs/: release, audit, and reproducibility documentation.

Reproducibility status

The phase scripts preserve the complete computational provenance of the active project. A portability pass is performed before public release to replace machine-specific assumptions in the final execution entry points. Raw and large intermediate matrices are reacquired from GEO rather than stored in Git.

Data and code availability

Public repository: https://github.com/rmaghembe1/UTI_HostOmics

Release v1.0.0 is archived in Zenodo with version DOI 10.5281/zenodo.21419897 and concept DOI 10.5281/zenodo.21419896.

Citation

Citation metadata are provided in CITATION.cff. The article DOI will be added after publication.

Licensing

Original analysis code is distributed under the MIT License. Original documentation, figure assemblies, and derived non-restricted tables are distributed under CC BY 4.0; see CONTENT_LICENSE.md. Third-party GEO source data are not redistributed and remain subject to their original terms.