{"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-14689"],"description":["To determine the binding sites of Zscan10, 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 ChIPmentation against HA."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 30 million mESCs were detached with 50,000 mESCs were detached with Accutase (Innovative Cell Technologies) and were cross-linked with 1% (vol/vol) formaldehyde in PBS for 10 min, and the reaction was quenched with Tris-HCl (200 mM, pH = 8).","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.","Library Construction - The fragmented chromatin was on-bead tagmented with pA-Tn5 (Protein Production and Structure Core Facility, EPFL) on a thermomixer at 37°C for 5 min with 800 rpm shaking. The chromatin was washed twice with low-salt wash buffer and was de-crosslinked with 1 µl Proteinase K (20 mg/ml) at 65°C and 1,400 rpm shaking overnight. DNA was purified with MinElute PCR purification kit (Qiagen, 28006) and was PCR amplified with Q5 High-Fidelity 2X Master Mix (New England Biolabs, M0492L) and indexed primers. The amplified library was cleaned-up by adding 1.2 times the volume of AMPureXP beads (Beckman Coulter, A63882) and eluted with 10 mM Tris-HCl, pH 8.0.","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).","Sequencing - The libraries were PE75 sequenced on an AVITI (Element Biosciences).","Nucleic Acid Extraction - The cross-linked nuclei were extracted and sonicated with the Covaris E220 Focused-ultrasonicator with the following settings: 20 min at 5% duty cycle, 140 W, 200 cycles."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - bigWig coverage tracks were generated from the resulting BAM files using the bamCoverage tool from deepTools (version 3.5.5) with a bin size of 1 bp and CPM normalisation.","Sequence Alignment - Raw reads were mapped to the mouse genome (mm10) using Bowtie2 (version 2.5.1), with the –sensitive-local mode."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Element AVITI"],"study_type":["ChIP-seq"],"species":["Mus musculus"],"pubmed_authors":["Wayo Matsushima"],"additional_accession":[]},"is_claimable":false,"name":"ChIPmentation of mESCs treated with dTAGv-1 to induce endogenous Zscan10 degradation","description":"To determine the binding sites of Zscan10, 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 ChIPmentation against HA.","dates":{"release":"2026-08-01T00:00:00Z","modification":"2026-08-01T01:01:02.988Z","creation":"2024-12-10T21:57:59.105Z"},"accession":"E-MTAB-14689","cross_references":{"ENA":["ERP166984"],"Biostudies":["E-MTAB-14692"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}