databaseArrayExpressfile_versionsfilesTxt J Donaldsoninstrument_platformIllumina HiSeq 2000speciesMus Musculussubmitter_keywordsChIP-seqfull_dataset_link Protocol - Rex1GFPd2 mouse ES cells were maintained in NDiff N2B27 media in the presence of CHIR99021 and PD0325901 as described in Yang et al., 2012. For time series of differentiation, the media containing inhibitor was removed and replaced with NDiff N2B27 media as time lindicated. ES cells were cross-linked as described in Lee et al., 2006. Yang SH, Kalkan T, Morrisroe C, Smith A, Sharrocks AD. (2012) PLoS Genet. 2012;8(12):e1003112. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation. Lee TI, Johnstone SE, Young RA. (2006) Nat Protoc. 1(2):729-48. Chromatin immunoprecipitation and microarray-based analysis of protein location. Library Construction - ChIP-seq was performed as described in Lee et al., 2006, with the following modifications. The crosslinked material was sheared by water bath sonication using bio-rupter for 45 mins, at high level, 30 secs on/ 30 secs off, 4 ⁰C. The size of sheared DNA fragments was between 100 bp to 600 bp, with median size around 300 bp. Immunoprecipitation was performed by incubating 0.75×107cells with 10 µg of H3K27Ac and H3K4me1 antibodies (Abcam; ab8895 and ab4729), respectively, cross-linked to dynabeads protein A (Invitrogen), overnight at 4 ⁰C. Lee TI, Johnstone SE, Young RA. (2006) Nat Protoc. 1(2):729-48. Chromatin immunoprecipitation and microarray-based analysis of protein location. Sequencing - About 10ng immunoprecipitated DNA for each sample was sent for sequencing.pubmed_abstractEmbryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-renewing conditions but comparatively less about how cells exit from this state in response to differentiation stimuli. Here, we examined the role of Otx2 in this process in mouse ESCs and demonstrate that it plays a leading role in remodeling the gene regulatory networks as cells exit from ground state pluripotency. Otx2 drives enhancer activation through affecting chromatin marks and the activity of associated genes. Mechanistically, Oct4 is required for Otx2 expression, and reciprocally, Otx2 is required for efficient Oct4 recruitment to many enhancer regions. Therefore, the Oct4-Otx2 regulatory axis actively establishes a new regulatory chromatin landscape during the early events that accompany exit from ground state pluripotency.pubmed_titleOtx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.pubmed_authorsYang Shen-Hsi SH, Kalkan Tüzer T, Morissroe Claire C, Marks Hendrik H, Stunnenberg Hendrik H, Smith Austin A, Sharrocks Andrew D ADsample_synonymsCo-Immunoprecipitations, type 2, extracellular signal-regulated kinase activity, pp44mapk, determination, Laboratory, Tyro5, Mpk2, D5Ertd135e, Mus domesticus, Parotid double-band protein, Pa, p42mapk, House Mouse, Long Term, Co Immunoprecipitation, LeMPK3, p44mpk, Dp38, 2, mitogen-activated protein kinase activity, Kinase, Sphingolipid activator protein 2, SAPK2, Effect, placement, A1 activator, adenomas, rabGAPLP, Salivary acidic proline-rich phosphoprotein 1|2, Pr1|Pr2, thymus nucleic acid, Genomes, pp42, ChIP, EK5, Co-Immunoprecipitation, Precipitation, RabGAP-5, nucleic acid library preparation, Swiss Mice, proteins, SAP-1, SAP-2, MP kinase activity, SecS, Immune, RUSC3, MBP kinase II activity, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], Double-Stranded DNA, house mouse, deoxyribonucleic acids, DNAn, Precipitations, “小鼠(mouse)” EXACT common_name [], ATP Phosphotransferases, Long-Term Effects, ATP, MAP kinase 2 activity, wide/broad, mouse, MYH-associated polyposis, ERK-2, Longterm Effect, autosomal recessive familial adenomatous polyposis, ERK1, ERK2, Saposin-A, Erk2, Parotid isoelectric focusing variant protein, PMK-2, Double-Stranded, PMK-1, antibodies, mice C57BL/6xCBA/CaJ hybrid, PMK-3, Fsrg1, 家鼠(house mouse), (Deoxyribonucleotide)n+m, RING3, p41mapk, count, MAPK, FSRG1, median, relational spatial quality, desoxyribose nucleic acid, autosomal recessive, MUTYH-associated polyposis, Mus musculus, MUTYH-related AFAP, RUTBC3, Transphosphorylases, Sphingolipid activator protein 1, Parotid proline-rich protein 1|2, mice, Sonications, CAPB, Swiss Mouse, p38, whole genome, domesticus, RABGAP5, C78273, sample., wide, Saposin-D, 9130208G10, Saposin-C, Saposin-B, p41, p40, multiple colorectal, ds DNA, microarray, MUTYH-related attenuated familial polyposis coli, Mouse, DNA, Db-F, location, time, Fsrg-1, 9030612K14Rik, Nat, NAT, D17H6S113E, DNS, SLA, (Deoxyribonucleotide)n, Effects, 小鼠(mouse), “家鼠(house mouse)” EXACT genbank_common_name [], number, broad, FSH, presence, Deoxyribonucleic acids, period, Db-s, Hek5, AA407128, Deoxyribonucleic Acid, House, Parotid acidic protein, Immune Precipitations, Mus musculus domesticus, Prkm1, p42-MAPK, Mice, familial adenomatous polyposis, Immune Precipitation, MAP, Map, ERK, PRKM1, PRKM2, Immunoprecipitation, Longterm, Swiss, Saposin-B-Val, familial adenomatous polyposis 2, Dispersin, PCBC, nucleic acid library construction, Double Stranded, Ring3, Long-Term, "mouse" EXACT common_name [], p42 mitogen-activated protein kinase activity, ATP:protein phosphotransferase (MAPKK-activated) activity, autosomal recessive multiple colorectal adenomas, "Mus muscaris" RELATED misnomer [], Component C, PIF-F, Long-Term Effect, AA986712, (Deoxyribonucleotide)m, STK26, p38-2, PIF-S, myelin basic protein kinase activity, RNAi screen, MUTYH-related attenuated familial adenomatous polyposis, DRT, MUTYH-Associated Polyposis, Peptide P-C, Proactivator polypeptide, DNAn+1, MAP-2 kinase activity, PRP-3|PRP-4, Co-beta-glucosidase, Cell, Phosphotransferases, Mus muscaris, p38delta, polypeptide, count in organism, Mus, MUTYH-related attenuated FAP, AW228947, Long Term Effects, chemical analysis, MBP kinase I activity, mKIAA4005, ds-DNA, Chromatin, PRP-1|PRP-2, D6S113E, Salivary acidic proline-rich phosphoprotein 3|4, waterbath, library construction, Kinases, mitogen activated kinase activity, P42MAPK, RNF3, Rnf3, Frg-1, Chromatin Immunoprecipitation, deoxyribonucleic acid, CSAct, House Mice, MAPK2, MYH-Associated Polyposis, RNAi screening, sample population, Longterm Effects, Laboratory Mice, "house mouse" EXACT genbank_common_name [], Cerebroside sulfate activator, AU018647, Protein C, ERT1, Protein A, EPHT3, Desoxyribonukleinsaeure, Sulfatide|GM1 activator, MAP syndrome, assay, quantitative, Laboratory Mouse, Glucosylceramidase activator, FAP2, MAP kinase 1 activity, presence or absence in organism, colorectal adenomatous polyposispubmed_title_synonymsMCOPS5, advanced, Drives, OCT4, Oct4, ESC, Oct3, OCT3, Otf3-rs7, Otf3g, Oct3|4, early, Oct-4, Oct-3, Otf-4, OTF-3, Otf-3, NF-A3, Oct-3|4, precocious, ES cell, reaction., Otf4, OTF4, Otf3, OTF3, CPHD6, activationdescription_synonymsChromatin, Mus musculus, Immunoprecipitation, Laboratory, ChIP, 小鼠(mouse), Swiss, “家鼠(house mouse)” EXACT genbank_common_name [], mice, Mus domesticus, mouse, Swiss Mouse, Chromatin Immunoprecipitation, House Mice, Swiss Mice, antibodies, "mouse" EXACT common_name [], House Mouse, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, Laboratory Mice, domesticus, "house mouse" EXACT genbank_common_name [], "Mus muscaris" RELATED misnomer [], 家鼠(house mouse), House, Mus, Mus musculus domesticus, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], Cell., Mouse, house mouse, “小鼠(mouse)” EXACT common_name [], Mice, Laboratory Mousename_synonymsStem Cells, Mouse Embryonic Stem, Mouse Embryonic, mESCs, Cells, Mouse Embryonic Stem Cell.pubmed_abstract_synonymsprojections, stria olfactoria lateralis, Networks, RP37, advanced, Modules, Gene Regulatory, multi-cellular organism, Materials, second cervical vertebra, Laboratory, lamellae, 小鼠(mouse), “家鼠(house mouse)” EXACT genbank_common_name [], Mus domesticus, Stem Cells, OCT4, Oct4, Gene, PNR, regulation of cellular transcription, stalk, Oct3, Network, OCT3, 身体, process of organ, House Mouse, protrusion, Oct-4, Oct-3, lamella, axis vertebra, lateral olfactory tract. body, 生物, Roles, House, Circuit, lateral olfactory tract, NF-A3, responsivity, Oct-3|4, tractus olfactorius lateralis, Transcriptional Networks, LOT, 多细胞生物, Concepts, Mus musculus domesticus, Transcriptional Network, Gene Regulatory Network, animal, Mice, Module, Chromatins, Transcriptional, reactivity, MCOPS5, rd7, Regulatory Network, Circuits, Genetic, 全身, cell, Swiss, Embryonic Stem Cell, C2, axis (CII), Swiss Mice, ridges, "mouse" EXACT common_name [], culm, "Mus muscaris" RELATED misnomer [], regulation of gene-specific transcription, DNA-dependent, vertebra 2, papilla, Role Concepts, Gene Network, chromosome scaffold, transcriptional control, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], house mouse, Otf4, OTF4, associated, Otf3, OTF3, “小鼠(mouse)” EXACT common_name [], laminae, 整个生物体, anatomical protrusion, body, axis, anatomical process, lamina, mouse, flanges, whole body, 躯体, C2 vertebra, RNR, Cistrons, Cell, Gene Circuits, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, Concept, 家鼠(house mouse), organism, cervical axis, Role Concept, Stem Cell, Mus, shelf, Role, precocious, Genetic Materials, regulation of transcription, flange, activation, Genetic Material, organ process, ESCS, Embryonic, Mus musculus, whole organism, Gene Circuit, Drives, Gene Module, 动物, mice, shelves, cervical vertebra 2, early., Swiss Mouse, House Mice, Otf3-rs7, axis [C II], Otf3g, projection, ridge, Oct3|4, Laboratory Mice, domesticus, "house mouse" EXACT genbank_common_name [], process, processes, olfactory tract, Otf-4, OTF-3, Otf-3, Gene Modules, Regulatory Networks, lateral olfactory stria, spine, Material, Gene Networks, Cells, Koerper, processus, Cistron, Mouse, response, CPHD6, Embryonic Stem, Laboratory Mouseview_count27isClaimabletruesearch_count42search_domainspatentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0reactome~0sra~33emdb~0wgs_masters~0ebiweb_resources~0ipd-mhc~0genome_assembly~0taxonomy~1ebiweb_people~0enzymeportal_enzymes~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0gpcrdb~0hgnc~0intact~0rhea~0imgt-hla~0patentnucleotides~0ensemblroot~0non-coding~0europepmc~0biosamples~7pubmed~1identifiers_registry~0pdbechem~0interpro~0biotools~0mesh~0coding~0efo~0project~0human_diseases~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0ebiweb_corporate~0omim~0sbo~0lrg~0ipd-kir~0rnacentral~0orcid_data_claims~0metagenomics~0pfam~0citation_count0citation_count_scaled0.0reanalysis_count_scaled0.0view_count_scaled0.008620689655172414download_count_scaled1.6009164357196475E-5download_count9normalized_connections0.294117647058824additional_accessionERP004709is_claimabletruenameH3K27Ac and H3K4me1 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell linedescriptionChromatin immunoprecipitation using H3K27Ac and H3K4me1 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)datespublication2014-06-24updated2014-06-24accessionE-MTAB-2282cross_referencespubmed24931607TAXONOMY10090