{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jasmina Al-Mousawi"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15452"],"description":["Single-embryo SMART-seq2 of mouse 2-cell stage embryos. The embryos have been generated with in vitro fertilization (IVF) and are staged as hours post-IVF."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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).","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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - For genes:  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.   For transposons:  TE expression analysis was performed as previously described (Formichetti et. al. 2025). To estimate TE expression, mapping parameters were adjusted: STAR was run using parameters: --outFilterMultimapNmax 5000 \\ --outSAMmultNmax 1 \\ --outFilterMismatchNmax 3 \\ --outMultimapperOrder Random \\ --winAnchorMultimapNmax 5000 \\ --alignEndsType EndToEnd \\ --alignIntronMax 1 \\ --alignMatesGapMax 350 \\ --seedSearchStartLmax 30 \\ --alignTranscriptsPerReadNmax 30000 \\ --alignWindowsPerReadNmax 30000 \\ --alignTranscriptsPerWindowNmax 300 \\ --seedPerReadNmax 3000 \\ --seedPerWindowNmax 300 \\ --seedNoneLociPerWindow 1000. Location of TEs was determined using the GRCm38/mm10 Repeatmasker annotation after removal of low complexity and simple repeats. Mapped reads were filtered such that only instances with both paired reads fully overlapping with the TE were considered for downstream analysis. Reads overlapping with gene bodies were also discarded to ensure that the read stemmed from the TE and not from the expression of an overlapping gene. Read quantification was performed using Featurecounts and options -p -B -s 0 --fracOverlap 1 -M to summarize across repeat names. For downstream analysis, all reads belonging to each repeat name were counted."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Vladimir Benes","Laura Villacorta","Jasmina Al-Mousawi","Ana Boskovic"],"additional_accession":[]},"is_claimable":false,"name":"High Resolution Mapping of Mouse Embryonic Genome Activation using SMART-seq2","description":"Single-embryo SMART-seq2 of mouse 2-cell stage embryos. The embryos have been generated with in vitro fertilization (IVF) and are staged as hours post-IVF.","dates":{"release":"2026-06-24T00:00:00Z","modification":"2026-06-24T14:21:12.717Z","creation":"2025-08-04T14:30:53.197Z"},"accession":"E-MTAB-15452","cross_references":{"ENA":["ERP177788"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}