title: R 3419
organism: Daphnia magna
description: Protocols: 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 Extraction Kit. Homogenization was conducted at 5 m/s for 10 s with FastPrep-24 (M.P. Biomedicals, Irvine, CA, USA) at room temperature. Prochloraz and endosulfan were purchased from Sigma Aldrich (St. Louis). Test solutions of EC5 and EC20, determined in preliminary tests according to OECD 202, were prepared with Elendt-M4 medium. 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. 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 (RNA > 10 ng/µl) was performed using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA), and quality control (RIN > 5.0) was conducted using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples were stored at -80 °C until mRNA sequencing. Total RNA was extracted from pooled Daphnia magna using the NucleoSpin RNA/Protein kit according to the manufacturer's protocol, and RNA quantity and purity were assessed with a NanoDrop 2000 spectrophotometer while integrity was evaluated on an Agilent 2100 Bioanalyzer using an RNA Pico Chip, with only samples showing RIN values of at least 5 proceeding to library preparation. Poly(A)-enriched, strand-specific mRNA libraries were then 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.
attributes.tag: ENA first public
attributes.value: 2026-02-28
attributes.tag: INSDC center name
attributes.value: Fraunhofer Institute for Molecular Biology and Applied Ecology
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-16432:R 3419
attributes.tag: age
attributes.value: 48
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: collection date
attributes.value: not collected
attributes.tag: condition
attributes.value: EC20
attributes.tag: developmental stage
attributes.value: juvenile stage
attributes.tag: extraction date
attributes.value: 09.05.25
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: individual
attributes.value: 10
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: body proper
attributes.tag: rin
attributes.value: 6.9
attributes.tag: sample name
attributes.value: E-MTAB-16432:R 3419
attributes.tag: scientific_name
attributes.value: Daphnia magna
attributes.tag: sex
attributes.value: female
attributes.tag: strain
attributes.value: Daphnia magna clone 5