Holtemme Gammarus ecotoxicogenomics research compendium

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This dataset is the frozen v1.0.1 research compendium supporting the Holtemme River field ecotoxicogenomics study of wild Gammarus pulex sampled across six transcriptomic sites spanning two wastewater-treatment-plant transitions in Germany. The compendium is organised into seven Data Packages (DP01–DP07) and contains processed analytical inputs, derived chemistry descriptors, RNA-seq quality-control and expression data, global transcriptome analyses, differential-expression outputs, functional enrichment and EchoGO v0.1.4 provenance, candidate-gene evidence, WGCNA network-selection evidence, site-associated module inference, publication-figure source data, Supplementary Information, rendered analysis reports, provenance records, validation outputs, and a frozen code snapshot. The primary LC-HRMS concentration data and upstream chemistry resources are maintained separately in the Holtemme chemistry archive (DOI: 10.5281/zenodo.22143080). Raw RNA-seq reads are available through NCBI SRA under accession SRP571512. The executable workflow is maintained at the associated GitHub repository: https://github.com/miloes114/holtemme-gammarus-ecotoxicogenomics. Version 1.0.1 synchronises the publication-facing artifacts with the submitted manuscript, including the final Figure 4 evidence-state legend, the corresponding rendered functional-synthesis report, the final Supplementary Information, and release metadata. The underlying scientific analyses, differential-expression results, functional evidence assignments, semantic-feature counts, WGCNA results, chemistry results, and frozen provenance are unchanged from v1.0.0. Original non-code research content in this compendium is licensed under CC BY 4.0 unless otherwise indicated. Source code is licensed under the MIT License. Third-party and externally archived resources retain their original licences and terms of use.

Authors 6

1. Camilo Escobar-Sierra Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

   Hidrobilógica SAS

2. Werner Brack

   Goethe University Frankfurt · Helmholtz Centre for Environmental Research

   Affiliation as printed

   Goethe University Frankfurt

   Helmholtz Centre for Environmental Research

3. Henner Hollert Aachen

   Goethe University Frankfurt · RWTH Aachen University

   Affiliation as printed

   Goethe-Universität Frankfurt am Main (Campus Riedberg)

   Rheinisch Westfälische Technische Hochschule Aachen RWTH Aachen Fakultät für Mathematik Informatik und Naturwissenschaften

4. Martin Krayer Von Krauss

   Helmholtz Centre for Environmental Research

   Affiliation as printed

   Helmholtz Centre for Environmental Research

5. Fabian G. Weichert

   Goethe University Frankfurt

   Affiliation as printed

   Goethe University Frankfurt

6. Pedro A. Inostroza Aachen

   University of Gothenburg · RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

   University of Gothenburg