{"id":"https://openalex.org/W7225466541","doi":"https://doi.org/10.64898/2026.11.06.764689","title":"SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag","display_name":"SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag","publication_year":2026,"publication_date":"2026-11-07","ids":{"openalex":"https://openalex.org/W7225466541","doi":"https://doi.org/10.64898/2026.11.06.764689"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.764689","doi":"https://doi.org/10.64898/2026.11.06.764689","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764689","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/07/2026.11.06.764689.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/07/2026.11.06.764689.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161186761","display_name":"Chao Yan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chao Yan","raw_affiliation_strings":["New York Genome Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center;","institution_ids":["https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009507025","display_name":"Ruiyang He","orcid":"https://orcid.org/0009-0001-8215-8439","observed_orcids":["https://orcid.org/0009-0001-8215-8439"]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruiyang He","raw_affiliation_strings":["New York Genome Center / Columbia University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center / Columbia University;","institution_ids":["https://openalex.org/I4210151462","https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161183128","display_name":"Sara Fernandez","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sara Fernandez","raw_affiliation_strings":["New York Genome Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center;","institution_ids":["https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042306442","display_name":"Maro\u0161 Ple\u0161ka","orcid":"https://orcid.org/0000-0001-7460-7479","observed_orcids":["https://orcid.org/0000-0001-7460-7479"]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maros Pleska","raw_affiliation_strings":["New York Genome Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center;","institution_ids":["https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033523264","display_name":"Silas Maniatis","orcid":"https://orcid.org/0000-0002-0888-1477","observed_orcids":["https://orcid.org/0000-0002-0888-1477"]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Silas Maniatis","raw_affiliation_strings":["New York Genome Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center;","institution_ids":["https://openalex.org/I4210151462"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046625423","display_name":"Ivan Raimondi","orcid":"https://orcid.org/0000-0002-9522-2794","observed_orcids":["https://orcid.org/0000-0002-9522-2794"]},"institutions":[{"id":"https://openalex.org/I4210151462","display_name":"New York Genome Center","ror":"https://ror.org/05wf2ga96","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210151462"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivan Raimondi","raw_affiliation_strings":["New York Genome Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New York Genome Center;","institution_ids":["https://openalex.org/I4210151462"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070436051","display_name":"Sanja Vickovi\u0107","orcid":"https://orcid.org/0000-0003-0985-9885","observed_orcids":["https://orcid.org/0000-0003-0985-9885"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sanja Vickovic","raw_affiliation_strings":["Columbia Unviersity"],"raw_orcid":"https://orcid.org/0000-0003-0985-9885","affiliations":[{"raw_affiliation_string":"Columbia Unviersity","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5070436051"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.51419997215271,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.51419997215271,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.44780001044273376,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.007300000172108412,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/spatial-epigenomics","display_name":"spatial epigenomics","score":0.9139999747276306},{"id":"https://openalex.org/keywords/poly-a-rna","display_name":"polyadenylated RNA","score":0.8740000128746033},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.9160000085830688},{"id":"https://openalex.org/keywords/h3k4me1","display_name":"H3K4me1","score":0.8700000047683716},{"id":"https://openalex.org/keywords/super-enhancers","display_name":"super-enhancers","score":0.9950000047683716},{"id":"https://openalex.org/keywords/neuroplasticity","display_name":"neuroplasticity","score":0.6859999895095825},{"id":"https://openalex.org/keywords/fiber-tracts","display_name":"fiber tracts","score":0.8029999732971191},{"id":"https://openalex.org/keywords/neocortex","display_name":"neocortex","score":0.9739999771118164},{"id":"https://openalex.org/keywords/chromatin-state","display_name":"chromatin state","score":0.6039999723434448}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.864799976348877},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6995000243186951},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.6790000200271606},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6542999744415283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6399000287055969},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6100999712944031},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.5781000256538391},{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.5526000261306763},{"id":"https://openalex.org/C119401833","wikidata":"https://www.wikidata.org/wiki/Q7802158","display_name":"Tiling array","level":5,"score":0.43959999084472656},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.42750000953674316},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4212000072002411},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.4023999869823456},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.39750000834465027},{"id":"https://openalex.org/C176619506","wikidata":"https://www.wikidata.org/wiki/Q5065899","display_name":"ChIP-sequencing","level":5,"score":0.3846000134944916},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.38100001215934753},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.37549999356269836},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.3628000020980835},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3149000108242035},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.31439998745918274},{"id":"https://openalex.org/C179463898","wikidata":"https://www.wikidata.org/wiki/Q10273301","display_name":"Epigenesis","level":5,"score":0.3061999976634979},{"id":"https://openalex.org/C56952853","wikidata":"https://www.wikidata.org/wiki/Q5773144","display_name":"Histone-modifying enzymes","level":5,"score":0.3034999966621399},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2985999882221222},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.29319998621940613},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.2919999957084656},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.28780001401901245},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.28760001063346863},{"id":"https://openalex.org/C2778901553","wikidata":"https://www.wikidata.org/wiki/Q238535","display_name":"5-Hydroxymethylcytosine","level":5,"score":0.2806999981403351},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.27250000834465027},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26969999074935913},{"id":"https://openalex.org/C101152365","wikidata":"https://www.wikidata.org/wiki/Q838135","display_name":"Histone H1","level":4,"score":0.2678000032901764},{"id":"https://openalex.org/C10058791","wikidata":"https://www.wikidata.org/wiki/Q910897","display_name":"Histone code","level":5,"score":0.2637999951839447},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.26100000739097595}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.764689","doi":"https://doi.org/10.64898/2026.11.06.764689","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764689","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/07/2026.11.06.764689.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.764689","doi":"https://doi.org/10.64898/2026.11.06.764689","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764689","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/07/2026.11.06.764689.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4000000059604645}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322128","display_name":"Svenska S\u00e4llskapet f\u00f6r Medicinsk Forskning","ror":"https://ror.org/0433fd238"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320324119","display_name":"Uppsala Universitet","ror":"https://ror.org/048a87296"},{"id":"https://openalex.org/F4320325677","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225466541.pdf","grobid_xml":"https://content.openalex.org/works/W7225466541.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W4229033508"],"related_works":["https://openalex.org/W4211162540","https://openalex.org/W4324344255","https://openalex.org/W4307114720","https://openalex.org/W4408727832","https://openalex.org/W4380272671","https://openalex.org/W4410345162","https://openalex.org/W4400121291","https://openalex.org/W4404064040","https://openalex.org/W7114802335","https://openalex.org/W7164661319"],"abstract_inverted_index":{"Spatial":[0],"epigenomics":[1],"maps":[2],"chromatin":[3,55,130,138],"states":[4],"within":[5],"intact":[6],"tissues,":[7],"yet":[8],"current":[9],"methods":[10],"remain":[11],"limited":[12],"by":[13],"accessibility":[14],"and":[15,53,65,72,92,154,169,184],"scale.":[16],"We":[17,77],"developed":[18],"SPACE-Tag,":[19],"a":[20],"spatial":[21,42,105,172],"CUT&Tag":[22],"framework":[23],"that":[24,146,180],"converts":[25],"epigenetic":[26],"marks-associated":[27],"DNA":[28],"into":[29],"polyadenylated":[30],"RNA":[31],"through":[32],"T7":[33],"based":[34],"linear":[35],"amplification,":[36],"enabling":[37],"direct":[38],"integration":[39],"with":[40,69,116,148],"standard":[41],"transcriptomic":[43],"workflows.":[44],"Applied":[45],"to":[46,101,108,156],"the":[47,84,93,98,103,119,134,165,176,187],"mouse":[48,86],"brain,":[49,87],"SPACETag":[50],"resolved":[51],"activating":[52],"repressive":[54],"landscapes,":[56],"recovered":[57],"region-specific":[58],"gene":[59],"regulatory":[60,178],"programs":[61],"across":[62,97],"anatomical":[63],"domains,":[64],"showed":[66,123,136],"strong":[67],"correlation":[68],"existing":[70],"bulk":[71],"single":[73],"cell":[74],"reference":[75],"data.":[76],"generated":[78],"an":[79,142],"integrated":[80],"multimodal":[81,106,168],"atlas":[82],"of":[83,158,167],"aging":[85,117,188],"profiling":[88],"five":[89],"histone":[90],"modifications":[91],"transcriptome":[94,139],"in":[95,118,174,186],"parallel":[96],"adult":[99],"lifespan":[100],"establish":[102],"largest":[104],"dataset":[107],"date.":[109],"This":[110],"analysis":[111],"uncovered":[112],"sharp":[113],"regional":[114],"divergence":[115],"brain:":[120],"fiber":[121],"tracts":[122],"widespread":[124],"transcriptional":[125],"downregulation,":[126],"often":[127],"without":[128],"nearby":[129],"state":[131],"transitions,":[132],"whereas":[133],"isocortex":[135],"coordinated":[137],"changes,":[140],"including":[141],"H3K4me1":[143],"peak":[144],"module":[145],"increased":[147],"age,":[149],"was":[150],"enriched":[151],"at":[152],"super-enhancers":[153],"linked":[155],"upregulation":[157],"neuronal":[159],"plasticity":[160],"regulators.":[161],"These":[162],"findings":[163],"highlight":[164],"power":[166],"high":[170],"throughput":[171],"genomics":[173],"uncovering":[175],"divergent":[177],"logic":[179],"governs":[181],"tissue-specific":[182],"vulnerability":[183],"resilience":[185],"brain.":[189]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-08T00:00:00"}