{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Wayo Matsushima"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16752"],"description":["To determine the effect of ZSCAN10 on genome-wide nucleosome occupancy patterns, mouse ES cells (mESCs) carrying Zscan10 gene endogenously tagged with 2xHA and an FKBP12(F36V) degron were treated with dTAGv-1 to induce ZSCAN10 degradation and were assayed with MNase-seq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - To induce the degradation of ZSCAN10 endogenously tagged with an FKBP12(F36V), the cells were cultured in medium containing either 500 nM dTAGv-1 (MedChemExpress, HY-145514) or the same volume of DMSO for 24 h prior to harvest.","Sample Collection - 1.5 million mESCs were detached by incubating in Accutase for 2 min at 37°C.","Growth Protocol - Mouse embryonic stem cells (mESCs) were cultured in 2i+LIF medium composed of DMEM (Thermo Fisher, 10566-024), 10% ES Cell FBS (Thermo Fisher, 16141079), 1X MEM Non-Essential Amino Acids Solution (Thermo Fisher, 11140050), 1 mM sodium pyruvate (Thermo Fisher, 11360-039), 100 µM 2-Mercaptoethanol (Thermo Fisher, 31350-010), 100 U/ml Penicillin-Streptomycin (Thermo Fisher, 15140-122), 100 ng/ml of mouse LIF (Protein Production and Structure Core Facility, EPFL), 3 μM of GSK3 inhibitor (CHIR99021; Tocris Biosciences, 4423), and 2 μM of MEK1/2 inhibitor (PD0325901; Tocris Biosciences, 4192).","Library Construction - The purified DNA was size-selected in a 1.5% agarose gel for fragments smaller than 200 bp. The DNA was then purified from gel, and 500 ng of it was used as input for library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S).","Nucleic Acid Extraction - Nuclear extraction and permeabilisation were performed on the detached cells in ATAC-RSB buffer containing 0.1% NP-40 and 0.1% Tween-20 on ice for 3 min. The nuclei were washed once with the same buffer and digested with 1 U MNase (Worthington Biochemical Corp., LS004798) in 50 µl buffer containing 1 mM CaCl2 at 37°C for 20 min on a thermomixer with 1,000 rpm mixing. The digested DNA was cleaned-up with DNA Clean and Concentrator-5 Kit (Zymo Research, D4014).","Sequencing - The libraries were PE75 sequenced on an AVITI (Element Biosciences)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw read mapping to mm10 was performed with Bowtie2 (version 2.5.1), with the --very-sensitive-local --no-discordant options.","Data Transformation - The alignment BAM files were used as input for the dpos function from DANPOS3 (version 3.0.0) to obtain genome-wide nucleosome occupancy values."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Element AVITI"],"study_type":["MNase-seq"],"species":["Mus musculus"],"pubmed_authors":["Wayo Matsushima"],"additional_accession":[]},"is_claimable":false,"name":"MNase-seq of mESCs treated with dTAGv-1 to induce endogenous ZSCAN10 degradation","description":"To determine the effect of ZSCAN10 on genome-wide nucleosome occupancy patterns, mouse ES cells (mESCs) carrying Zscan10 gene endogenously tagged with 2xHA and an FKBP12(F36V) degron were treated with dTAGv-1 to induce ZSCAN10 degradation and were assayed with MNase-seq.","dates":{"release":"2026-09-08T00:00:00Z","modification":"2026-09-08T10:15:55.33Z","creation":"2026-03-12T14:02:08.079Z"},"accession":"E-MTAB-16752","cross_references":{"ENA":["ERP190726"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0003751","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}