{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alexandra Loll"],"organism":["Daphnia magna"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17707"],"description":["The experiment investigates how abamectin, chlorpyrifos, nicotine, pyriproxyfen and thiacloprid affect the gene expression in the freshwater invertebrate Daphnia magna. The experiment aimed to distinguish 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 sublethal effect concentrations for each substance, which were then used as exposure levels in subsequent assays so that molecular changes could be characterized. Pooled animals from the low and high exposure groups and corresponding controls were sampled after 48 hours for whole-animal RNA extraction, and poly(A)-enriched RNA was sequenced on an Illumina platform, followe"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Poly(A)-enriched, strand-specific mRNA libraries were generated by the sequencing provider (NGS-Services for Integrative Genomics, University of Göttingen or Eurofins Genomics Germany GmbH, Ebersberg) 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.","Sample Treatment - Test solutions were prepared with Elendt-M4 medium. Subsequently, 40 mL of each test solution were transferred to three test vessels (replicates) and analogously 40 mL of pure Elendt-M4 medium were used as control samples. 20 juvenile daphnia were transferred to the test vessels. Incubation was carried out in accordance with OECD 202 in complete darkness over a period of 48 hours.","Nucleic Acid Extraction - Total RNA and protein were extracted according to the NucleoSpin® RNA/Protein extraction kit (NucleoSpin® RNA/Protein, Macherey-Nagel GmbH & Co. KG, Düren, Germany). RNA quantification was performed using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA), and quality control was conducted using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples were stored at -20 °C until mRNA sequencing.","Sequencing - The resulting libraries were sequenced as 50bp single-reads on an Illumina HiSeq 4000 platform (abamectin, chlorpyrifos) or as 150 bp paired-end reads on an Illumina NovaSeq 6000 platform (nicotine, pyriproxyfe, thiacloprid) at a target depth of approximately 30 million reads/read pairs per sample. Sequencing was conducted by NGS-Services for Integrative Genomics, University of Göttingen for abamectin, chlorpyrifos and pyriproxyfen and by Eurofins Genomics Germany GmbH, Ebersberg for nicotine and thiacloprid.","Sample Collection - For each sample, 10 daphnia were randomly transferred from the test vessel into a tube. After adding the lysis buffer (NucleoSpin® RNA/Protein, Macherey-Nagel GmbH & Co. KG, Düren, Germany), lysis was performed according to the manufacturer's protocol for the NucleoSpin® RNA/Protein extraction kit. Homogenization was conducted at 5 m/s for 10 s with FastPrep-24 (M.P. Biomedicals, Irvine, CA, USA) at room temperature."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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 independen","Sequence Alignment - Alignment of raw reads was performed to the Daphnia magna reference genome assembly Daphmag2.4 (GCA_001632505.1). Reads were mapped with the STAR spliced read aligner using its genome-guided splice-aware algorithm to place reads across exon–exon junctions, and the resulting gene-level count data from STAR were used as input for downstream DESeq2-based differential expression analysis; alignment quality and mapping performance were assessed by standard STAR and RNA‑seq QC outputs prior to statistical analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["see manuscript","NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel).","Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB","Illumina NovaSeq 6000","FastPrep‑24 homogenizer (MP Biomedicals)"],"study_type":["RNA-seq of coding RNA"],"species":["Daphnia magna"],"pubmed_authors":["Sebastian Eilebrecht","Alexandra Loll"],"additional_accession":[]},"is_claimable":false,"name":"mRNA-Seq of Daphnia magna exposed to abamectin, chlorpyrifos, nicotine, pyriproxyfen and thiacloprid against untreated control groups","description":"The experiment investigates how abamectin, chlorpyrifos, nicotine, pyriproxyfen and thiacloprid affect the gene expression in the freshwater invertebrate Daphnia magna. The experiment aimed to distinguish 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 sublethal effect concentrations for each substance, which were then used as exposure levels in subsequent assays so that molecular changes could be characterized. Pooled animals from the low and high exposure groups and corresponding controls were sampled after 48 hours for whole-animal RNA extraction, and poly(A)-enriched RNA was sequenced on an Illumina platform, followe","dates":{"release":"2026-09-30T00:00:00Z","modification":"2026-09-30T01:01:15.359Z","creation":"2026-09-25T07:18:02.406Z"},"accession":"E-MTAB-17707","cross_references":{"ENA":["ERP206866"],"Biostudies":["E-MTAB-17689"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}