Unknown,Transcriptomics,Genomics,Proteomics

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MRNA-Seq of Lemna minor exposed to different concentrations of sucralose against untreated control groups

ABSTRACT: The experiment investigates how the artificial sweetener sucralose affects gene expression in the teleost fish Danio rerio in order to derive mechanistic information relevant for environmental risk assessment. The main test including transcriptomics, was conducted with 10 µg/L and 100 mg/L as test concentrations. Whole plant tissue from each exposure group and corresponding controls was sampled after 7 days for RNA extraction, and poly(A)-enriched RNA was sequenced (paired-end, 150 bp) on an Illumina NovaSeq platform, followed by alignment to the Lemna minor reference genome and differential expression analysis using a DESeq2-based workflow with independent hypothesis weighting, data-driven log2 fold-change thresholds, and multiple-testing correction to define robust sets of differentially expressed genes per substance and concentration. Overrepresentation analysis of Gene Ontology terms using a common detected-gene background then mapped these gene-level changes to biological processes.

INSTRUMENT(S): Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB, RapidPURE RNA Plant Kit (MP Biomedicals, Illkirch, France), Illumina NovaSeq 6000, FastPrep-24 homogeniser

ORGANISM(S): Lemna minor

SUBMITTER: Alexandra Loll

PROVIDER: E-MTAB-16758 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The experiment investigates how the azole fungicide prochloraz and the organochlorine insecticide endosulfan affect behavior and gene expression in the freshwater invertebrate Daphnia magna in order to distinguish endocrine from neurotoxic mechanisms and derive mechanistic information relevant for environmental risk assessment. Juvenile D. magna were first subjected to acute immobilization tests following OECD Guideline 202 to establish 48‑hour EC5 and EC20 effect concentrations for each pesticide, which were then used as sublethal exposure levels in subsequent assays so that molecular and behavioral changes could be characterized below overt toxicity. At these sublethal concentrations, swimming activity was quantified in a 24‑well plate setup using automated video tracking to assess concentration-dependent changes in activity time as an organism-level functional endpoint sensitive to both metabolic and neurotoxic disturbance. In parallel, pooled animals from the EC5 and EC20 exposure groups and corresponding controls were sampled after 48 hours for whole-animal RNA extraction, and poly(A)-enriched RNA was sequenced (paired-end, 150 bp) on an Illumina NovaSeq platform, followed by alignment to the Daphnia magna reference genome and differential expression analysis using a DESeq2-based workflow with independent hypothesis weighting, data-driven log2 fold-change thresholds, and multiple-testing correction to define robust sets of differentially expressed genes per substance and concentration. Overrepresentation analysis of Gene Ontology terms using a common detected-gene background then mapped these gene-level changes to biological processes, revealing prochloraz-associated enrichment of lipid, steroid and sterol metabolic pathways and endosulfan-associated enrichment of ion transport and signaling-related processes, thereby providing mode-of-action–consistent toxicogenomic signatures that mechanistically complement the observed behavioral phenotypes.

Dataset Information

MRNA-Seq of Lemna minor exposed to different concentrations of sucralose against untreated control groups

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