biostudies-arrayexpressAlexandra LollLemna minorhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16758The 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.biostudies-arrayexpressSample Treatment - Sucralose (CAS 56038-13-2, purity 98%) was purchased from abcr. Test solutions of 10 µg/L and 100 mg/L were prepared with Steinberg medium. 150 mL of each test solution were transferred to three test vessels (replicates) and analogously 150 mL of Steinberg medium were used as control samples. 4 plant with 3 fronds each were transferred to the test vessels. Incubation was carried out in accordance with OECD 221 at 24±2 °C and continous light.Sequencing - Sequencing was conducted by Novogene. Paired-end sequencing was performed using Illumina’s NovaSeq 6000 (Illumina Inc., San Diego, CA, USA). The read length was 150 base pairs.Library Construction - Poly(A)-enriched, strand-specific mRNA libraries were generated by the sequencing provider (Novogene) using a standard Illumina-compatible workflow comprising poly(A) selection, RNA fragmentation, first- and second-strand cDNA synthesis, adapter ligation, PCR amplification and size selection, and the resulting libraries were sequenced as 150 bp paired-end reads on an Illumina NovaSeq 6000 platform at a target depth of approximately 30 million read pairs per sample.Sample Collection - For each sample, 30 mg of plant tissue were randomly collected from the test vessel into a tube. After adding the lysis matrix (¼ Ceramic Sphere, MP Biomedicals), the lysis was performed according to the manufacturer’s protocol of the RapidPURE RNA Plant Kit (MP Biomedicals Illkirch, France). Homogenization was conducted at 5 m/s for 60 s with FastPrep-24© 5G (MP Biomedicals Illkirch, France) at room temperature.Growth Protocol - One week before test start, a pre-culture of Lemna minor was auxenically prepared from a stock culture in Steinberg medium according to OECD TG 221. Plants were kept in a growth chamber at 24±2°C and under continuous light (85-135 µE∙m-2∙s-1).Nucleic Acid Extraction - Total RNA and protein were extracted according to the RapidPURE Plant Kit (MP Biomedicals Illkirch, France). RNA quantification (RNA>100 ng/µL) was performed using Nanodrop 2000 spectrophotometer (Thermo Scientific), and quality control (RIN>7.0) was conducted using the 2100 Bioanalyzer (Agilent Technologies). The samples were stored at -20°C until mRNA sequencing.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Normalization and data transformation followed a DESeq2-based RNA‑seq workflow: raw gene-level count matrices from STAR alignments were imported and merged, then low-abundance genes were removed using a counts-per-million–based relevance threshold applied per experimental condition to restrict analysis to robustly detected features. Size factors and gene-wise dispersions were estimated with DESeq2’s default negative binomial modeling, and Wald tests were performed in a design including exposure condition as the main factor to obtain normalized counts and test statistics for each contrast. Log2 fold changes were then shrunk using apeglm to stabilize effect-size estimates for low-count or highly variable genes, and multiple testing was controlled by combining independent hypothesis weighting with Benjamini–Hochberg adjustment to obtain adjusted p values and q values; genes were considered differentially expressed when the adjusted p value was below 0.05 and the absolute log2 fold change exceeded a data-driven cutoff defined as the upper 30th percentile of the absolute log2 fold-change distribution, with quality-control diagnostics (normalization and dispersion plots, p value and log2 fold-change distributions, sample distance matrices, and PCA/t‑SNE) used to verify normalization performance.Sequence Alignment - Adapter sequences were removed using trimmomatic (v0.39) and library’s sequence quality was assessed with FastQC (v0.11.5). Reads were checked for potential contaminations with FastQ Screen (v0.14.1) using bowtie2 (v2.3.2) against the genome 2019v2 (lemna.org) and corresponding genome annotation file (GTF) [https://genomevolution.org/coge/LoadGenome.pl?wid=47218] using STAR aligner (v2.5.2a) allowing for 2 mismatches within 50 bases. Feature mapped reads were counted with featureCounts (v2.0.1).UnknownTranscriptomicsGenomicsProteomicsDell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GBRapidPURE RNA Plant Kit (MP Biomedicals, Illkirch, France)Illumina NovaSeq 6000FastPrep-24 homogeniserRNA-seq of coding RNALemna minorSebastian EilebrechtAlexandra LollfalsemRNA-Seq of Lemna minor exposed to different concentrations of sucralose against untreated control groupsThe 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.2026-04-30T00:00:00Z2026-04-30T01:01:48.183Z2026-03-17T10:49:29.441ZE-MTAB-16758ERP190864EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969