biostudies-arrayexpressJasmina Al-MousawiMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15454RNA-seq of single mouse embryos using SMART-seq2. The embryos have been generated with IVF and are staged as hours post-IVF. At the zygote stage (~ 4h post-IVF), the embryos have been microinjected with 1.7 μg/μL Kdm5b wild-type (WT) or catalytic mutant (CM) mRNA. Non-injected embryos are denoted as “Noninj”. The embryos were cultured until collection at 20 h, 23 h, and 26 h post-IVF. A note on replicates: The replicate annotation refers to the number of times the specific condition was collected, i.e., the N number. It does not reflect the experimental batch. For the IVF batch, please refer to the sample sheet provided in the accompanying Git repository.biostudies-arrayexpressSample Collection - At the appropriate stage, embryos were washed in 37°C M2. Embryos were collected individually using a mouth pipette and lysed. Samples were stored at -20°C until library preparation.Sequencing - The libraries were pooled and sequenced on a NextSeq500 Sequencer using 40 bp read lengths in paired-end mode. The individual libraries were sequenced to an average depth of 5 million reads per sample.Nucleic Acid Extraction - The RNA was reverse transcribed to generate cDNA and purified with a 0.6 x ratio of SPRIselect beads according to previously published protocols (Picelli et. al. 2014, Hennig et. al. 2018).Sample Treatment - Microinjections were performed between 4-6 h after IVF using an Eppendorf Femtojet system with a Leica iDM8 microscope. Zygotes were washed in warm M2 media and placed in an M2 drop under mineral oil. Kdm5b WT and CM mRNAs were microinjected into the cytoplasm of zygotes at 1.7 μg/μL.Library Construction - SMART-seq2 libraries were prepared by the EMBL Genecore Facility, as previously described protocols (Picelli et. al. 2014, Hennig et. al. 2018).Growth Protocol - IVF was performed according to (Guan et.al. 2014) with a co-incubation of oocytes and sperm adjusted to 2 h for precision staging. Embryos were cultured in equilibrated KSOM under 20 % O₂ and 5% CO₂ at 37°C up to the 2-cell stage.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Fastq files were mapped to the GRCm38/mm10 genome containing only major chromosomes (chr1-18, X, Y and MT) using STAR. For SMART-seq2 data generated in this study, paired-end reads were mapped using alignreads mode with the following parameters: --outFilterMultimapNmax 20 \ --outFilterMultimapScoreRange 0 \ --outFilterMismatchNoverLmax 0.05 \ --sjdbScore 2. Read quantification was performed using Featurecounts and options -p --countReadPairs.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAMus musculusVladimir BenesLaura VillacortaJasmina Al-MousawiAna BoskovicfalseTime course of Embryonic Genome Activation Following Kdm5b Overexpression using SMART-seq2RNA-seq of single mouse embryos using SMART-seq2. The embryos have been generated with IVF and are staged as hours post-IVF. At the zygote stage (~ 4h post-IVF), the embryos have been microinjected with 1.7 μg/μL Kdm5b wild-type (WT) or catalytic mutant (CM) mRNA. Non-injected embryos are denoted as “Noninj”. The embryos were cultured until collection at 20 h, 23 h, and 26 h post-IVF. A note on replicates: The replicate annotation refers to the number of times the specific condition was collected, i.e., the N number. It does not reflect the experimental batch. For the IVF batch, please refer to the sample sheet provided in the accompanying Git repository.2026-06-24T00:00:00Z2026-06-24T14:20:39.066Z2025-08-06T11:53:05.038ZE-MTAB-15454ERP177885EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0003969EFO_0004184