Commercial Glyphosate Formulations Exceed Active Ingredient Toxicity via Mitochondrial ROS and Transcriptomic Disruption

Published: 27 October 2025| Version 1 | DOI: 10.17632/pj6t7hbpp4.1
Contributor:
Maria Bonfleur

Description

This dataset contains RNA sequencing (RNAseq) tables derived from HepG2 human liver carcinoma cells exposed to glyphosate (GLY) or a glyphosate-based herbicide (GBH). The research aimed to investigate whether the GBH formulation exerts greater cellular toxicity than GLY alone. The dataset includes normalized gene expression values and differential expression analysis comparing control, GLY-treated, and GBH-treated samples. These data can be used to explore transcriptional changes, identify affected pathways, and further investigate mechanisms of GBH-induced toxicity. Overall, the RNAseq results indicate that GBH exposure leads to broader transcriptional alterations than GLY, involving genes related to oxidative stress, endoplasmic reticulum (ER) stress, autophagy, and apoptosis. The dataset provides a valuable resource for researchers studying the molecular responses to glyphosate-based herbicides.

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For RNAseq analysis, total RNA was isolated from HepG2 cell lines after treatment with 100 ppm of GLY or GBH for 24 h. RNA samples were diluted in RNase-free water and 5 µl of RNA samples were sent for sequencing, which was performed by Novogene (Novogene GmbH, Cambridge, UK). The quantity and quality of the RNA samples were assessed using the following methods. Preliminary quality control was performed on 1% agarose gel electrophoresis to test RNA degradation and potential contamination. Sample purity and preliminary quantitation were measured using Bioanalyzer 2100 (Agilent Technologies, USA) and it was also used to check the RNA integrity and final quantitation. For library preparation, we used the Novogene NGS RNA Library Prep Set (PT042). The mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNA enrichment. Subsequently, mRNA was randomly fragmented, and cDNA synthesis proceeded using random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain is finished, the second chain is synthesized with the addition of an Illumina buffer (non-directional library preparation). With this and together with the presence of dNTPs, RNase H and polymerase I from E. Coli, the second chain will be obtained by Nick translation. The resulting products go through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries were pooled and sequenced on the Illumina Novaseq X platform, according to effective library concentration and data amount using the paired-end 150 strategy (PE150).

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Molecular Biology, Toxicology, Environmental Science, Cell Biology, Transcriptomics

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