{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nils Niepagen"],"organism":["Hippoglossus hippoglossus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15858"],"description":["This 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library 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 sequencing","Sequencing - 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 genome","Sample 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 extraction","Nucleic 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 ± 0.24"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NanoDrop spectrophotometer, Agilent 2100 Bioanalyzer","Agilent 2100 Bioanalyzer (Agilent Technologies); Qubit Fluorometer (Thermo Fisher Scientific); standard electrophoresis system","standard computational workstation","none","Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Hippoglossus hippoglossus"],"pubmed_authors":["Nils Niepagen"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of maternal provisioning and zygotic genome activation during early Atlantic halibut (Hippoglossus hippoglossus) embryogenesis","description":"This 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.","dates":{"release":"2025-11-29T00:00:00Z","modification":"2025-11-29T02:02:23.586Z","creation":"2025-10-24T15:05:27.566Z"},"accession":"E-MTAB-15858","cross_references":{"ENA":["ERP182907"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003738","EFO_0004184"]}}