biostudies-arrayexpressNils NiepagenHippoglossus hippoglossushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15858This study investigates transcriptomic changes across early embryonic development in Atlantic halibut (Hippoglossus hippoglossus), spanning stages from unfertilized eggs to late epiboly. RNA-seq was performed on whole embryos from three females at seven developmental stages to characterize maternal mRNA provisioning and zygotic genome activation. The data provide a comprehensive overview of gene expression dynamics during halibut embryogenesis and represent a resource for understanding early developmental regulation in teleosts.biostudies-arrayexpressLibrary Construction - mRNA libraries were prepared by Novogene Co. (Beijing, China) using their standard Illumina TruSeq RNA Sample Preparation protocol, following manufacturer guidelines for paired-end sequencing. Libraries were quality-checked by agarose gel electrophoresis and Bioanalyzer QC prior to sequencingSequencing - Sequencing was performed by Novogene Co. on an Illumina HiSeq 2500 platform using paired-end 150 bp reads. Library and run quality were assessed with Nanodrop and Agilent 2100 QC before sequencing. Data quality was verified with FastQC; average ~57 million high-quality reads per sample with > 92 % mapping rate to the Atlantic halibut reference genomeSample Collection - Atlantic halibut eggs were obtained from broodstock at Nordic Halibut AS (Midsund, Norway). Good-quality egg batches from four females were fertilized using cryopreserved milt and incubated in 250 L seawater incubators at 6 °C and 34 ppt salinity. Eggs were sampled at defined developmental stages (unfertilized, 8-cell, 16-cell, blastula, 25 % epiboly, 50 dd), placed in cryovials, snap frozen in liquid nitrogen, and stored at −80 °C until RNA extractionNucleic Acid Extraction - Total RNA was extracted from pools of 10 eggs per sample using the RNeasy Universal Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA concentration was measured with a NanoDrop spectrophotometer, and RNA integrity (RIN) was assessed on an Agilent 2100 Bioanalyzer, yielding mean RIN = 9.8 ± 0.24OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSequence Alignment - For sample N102, the deposited paired-end FASTQ files (N102_1_recreated.fq.gz, N102_2_recreated.fq.gz) were reconstructed from alignment BAM files (accepted_hits.bam and unmapped.bam) after the original raw reads were lost. The original FASTQ data were used for all analyses reported in the manuscript; reconstructed files contain the same reads for reproducibility.UnknownTranscriptomicsGenomicsProteomicsNanoDrop spectrophotometer, Agilent 2100 BioanalyzerAgilent 2100 Bioanalyzer (Agilent Technologies); Qubit Fluorometer (Thermo Fisher Scientific); standard electrophoresis systemstandard computational workstationnoneIllumina HiSeq 2000RNA-seq of coding RNAHippoglossus hippoglossusNils NiepagenfalseRNA-seq analysis of maternal provisioning and zygotic genome activation during early Atlantic halibut (Hippoglossus hippoglossus) embryogenesisThis study investigates transcriptomic changes across early embryonic development in Atlantic halibut (Hippoglossus hippoglossus), spanning stages from unfertilized eggs to late epiboly. RNA-seq was performed on whole embryos from three females at seven developmental stages to characterize maternal mRNA provisioning and zygotic genome activation. The data provide a comprehensive overview of gene expression dynamics during halibut embryogenesis and represent a resource for understanding early developmental regulation in teleosts.2025-11-29T00:00:00Z2025-11-29T02:02:23.586Z2025-10-24T15:05:27.566ZE-MTAB-15858ERP182907EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003738EFO_0004184