{"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-16935"],"description":["Single-embryo SMART-seq of mouse Embryonic Genome Activation with 2-cell stage embryos collected after 2 h precision in vitro fertilization (IVF) at the following timepoints: 17, 20, 23, and 26 h post-IVF. Individual embryos were lysed in total cell lysis buffer, and the lysates were split to perform in vitro polyadenylation on half of the sample. SMART-seq2 libraries were generated subsequently. All samples have matched in vitro polyadenylated (PolyA+) and nonadenylated (PolyA-) libraries."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was purified using a 2.2x ratio of RNAClean XP beads. Beads were washed three times with 80% ethanol and then RNA was eluted in 10μL RNAse-free water. From each sample, 5μL RNA underwent in-vitro polyadenylation and 5μL were subjected to the same processing, but omitting the Poly(A) Polymerase. RNA was mixed with 1μL 10X E. coli Poly(A) Polymerase Reaction Buffer, 1μL 10mm ATP, 0.25μL SUPERase RNAse inhibitor, 2.5μL RNAse-free water, 0.25μL E. coli Poly(A) Polymerase. Samples were incubated at 37°C for 30 min and then kept at 4°C. Then RNA was bead-purified again as described above with a 2.2x ratio of RNAClean XP beads and eluted in 10μL RNAse-free water containing 2.5mM dNTPs and 2.5 μM anchored oligo-dT.","Sample Treatment - The treatment was performed on half of the sample lysates with Poly(A) polymerase. See nucleic acid extraction protocol for details.","Library Construction - 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).","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.","Sample Collection - At the appropriate stage, embryos were washed in 37°C M2. Embryos were collected individually using a mouth pipette and lysed. Embryos were collected individually using a mouth pipette and lysed in 10 μL in 1x total cell lysis (TCL) buffer containing 1% β-mercaptoethanol. Samples were stored at -80°C until library preparation.","Sequencing - Samples were pooled and sequenced on a NextSeq2000 sequencer using 50 bp read lengths in paired-end mode. Polyadenylated samples were sequenced twice because they were undersequenced in the first run, resulting in 4 raw data files. For the second sequencing run, libraries were prepared from cDNA again. Thus, the barcoding of individual polyadenylated samples varies across sequencing runs."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Vladimir Benes","Laura Villacorta","Luca Michetti","Jasmina Al-Mousawi","Ana Boskovic"],"additional_accession":[]},"is_claimable":false,"name":"High Resolution Mapping of Mouse Embryonic Genome Activation using SMART-seq2 with in vitro polyadenylation","description":"Single-embryo SMART-seq of mouse Embryonic Genome Activation with 2-cell stage embryos collected after 2 h precision in vitro fertilization (IVF) at the following timepoints: 17, 20, 23, and 26 h post-IVF. Individual embryos were lysed in total cell lysis buffer, and the lysates were split to perform in vitro polyadenylation on half of the sample. SMART-seq2 libraries were generated subsequently. All samples have matched in vitro polyadenylated (PolyA+) and nonadenylated (PolyA-) libraries.","dates":{"release":"2026-06-24T00:00:00Z","modification":"2026-06-24T14:19:32.976Z","creation":"2026-04-20T14:27:54.726Z"},"accession":"E-MTAB-16935","cross_references":{"ENA":["ERP192367"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0003969","EFO_0004184"]}}