biostudies-arrayexpressJule BäckerDanio reriohttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16491In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide boscalid (CAS 188425-85-6). Zebrafish embryos were exposed to boscalid according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.biostudies-arrayexpressSequencing - samples were sequenced using Illumina NovaSeq 6000 System to obtain 30 million 150 bp paired-end raw reads per sample.Sample Treatment - three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub-lethal concentrations of boscalid in addition to untreated control groups.Sample Collection - at the end of exposure, 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep-24 homogeniser (MP Biomedicals, Irvine, USA) at 5 m/s speed for 45 seconds.Growth Protocol - Zebrafish embryos were exposed to boscalid for 96 hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours.Library Construction - RNA libraries were prepared from RNA extracts with RNA integrity number (RIN) values > 8.5 using poly(A) RNA purification followed by fragmentation. Using reverse transcription, cDNA libraries was produced from mRNA fragments and ligated to the adapters.Nucleic Acid Extraction - total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit (Macherey & Nagel, Düren, Germany). According to the manufacturer’s protocol. Nanodrop 2000 spectrophotometer (Thermo Scientific) was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System (Agilent, Santa Clara, USA). Samples were stored at -80°C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - adapter sequences were removed using Fastp v0.23.2 and raw reads were aligned to Danio rerio reference genome (assembly GRCz11) using STAR aligner v.2.7.5b . followed by read counting with quantMode GeneCounts function in STAR to obtain count per gene tables.Data Transformation - the count per gene tables obtained from quantMode GeneCounts function in STAR were compiled in R (v 4.0.5) in one count matrix (Boscalid_CountMatrix.txt) where rows correspond to genes and columns to the sample. Low abundant read counts with less than 1 count per million reads were removed. Following this, reads were normalized to obtain the normalized count table (Boscalid_DESeqNormCounts.txt) and differential gene expression analysis was performed using DESeq2 (version 1.30.1).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNADanio rerioCimin KalaliFatma MarghanyJule BäckerSebastian EilebrechtHenner HollertHannes ReinwaldChristoph SchäfersJulia AlvinczPragya ThapaliyafalsemRNA-Seq of Danio rerio exposed to different concentrations of the fungicide boscalid against untreated control groupsIn the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide boscalid (CAS 188425-85-6). Zebrafish embryos were exposed to boscalid according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.2026-09-30T00:00:00Z2026-09-30T01:00:42.878Z2026-01-02T15:02:11.442ZE-MTAB-16491ERP187211EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969