{"id":"https://openalex.org/W4394560315","doi":"https://doi.org/10.6084/m9.figshare.14332859","title":"Cell type-specific chromatin accessibility analysis in the mouse and human brain","display_name":"Cell type-specific chromatin accessibility analysis in the mouse and human brain","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W4394560315","doi":"https://doi.org/10.6084/m9.figshare.14332859"},"language":"en","primary_location":{"id":"pmh:oai:figshare.com:article/14332859","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Cell_type-specific_chromatin_accessibility_analysis_in_the_mouse_and_human_brain/14332859","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},"volume":null,"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/dataset/Cell_type-specific_chromatin_accessibility_analysis_in_the_mouse_and_human_brain/14332859","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048308048","display_name":"Devin Rocks","orcid":"https://orcid.org/0000-0002-3192-0219","observed_orcids":["https://orcid.org/0000-0002-3192-0219"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rocks, Devin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052594738","display_name":"Ivana Jari\u0107","orcid":"https://orcid.org/0000-0002-8818-2974","observed_orcids":["https://orcid.org/0000-0002-8818-2974"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jaric, Ivana","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010165541","display_name":"Lydia Tesfa","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tesfa, Lydia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048839844","display_name":"John M. Greally","orcid":"https://orcid.org/0000-0001-6069-7960","observed_orcids":["https://orcid.org/0000-0001-6069-7960"]},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greally, John M.","raw_affiliation_strings":["Albert Einstein College of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040370543","display_name":"Masako Suzuki","orcid":"https://orcid.org/0000-0003-0605-9225","observed_orcids":["https://orcid.org/0000-0003-0605-9225"]},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suzuki, Masako","raw_affiliation_strings":["Albert Einstein College of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine","institution_ids":["https://openalex.org/I129975664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089796357","display_name":"Marija Kundakovi\u0107","orcid":"https://orcid.org/0000-0002-6734-4217","observed_orcids":["https://orcid.org/0000-0002-6734-4217"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kundakovic, Marija","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9613999724388123,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9613999724388123,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.01590000092983246,"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":0.009999999776482582,"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/chromatin-accessibility","display_name":"chromatin accessibility","score":0.9620000123977661},{"id":"https://openalex.org/keywords/atac-seq","display_name":"ATAC-seq","score":0.8989999890327454},{"id":"https://openalex.org/keywords/cryopreservation","display_name":"cryopreservation","score":0.9200000166893005},{"id":"https://openalex.org/keywords/postmortem-brain","display_name":"postmortem brain","score":0.7850000262260437},{"id":"https://openalex.org/keywords/mouse-brain","display_name":"mouse brain","score":0.7509999871253967},{"id":"https://openalex.org/keywords/neurons","display_name":"neurons","score":0.6259999871253967},{"id":"https://openalex.org/keywords/cell-type-specific-epigenetics","display_name":"cell-type-specific epigenetics","score":0.6800000071525574},{"id":"https://openalex.org/keywords/open-chromatin-regions","display_name":"open chromatin regions","score":0.8960000276565552}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7254737615585327},{"id":"https://openalex.org/C2778144876","wikidata":"https://www.wikidata.org/wiki/Q4955745","display_name":"Brain Cell","level":2,"score":0.5244463086128235},{"id":"https://openalex.org/C2777670902","wikidata":"https://www.wikidata.org/wiki/Q492038","display_name":"Human brain","level":2,"score":0.4972522556781769},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43993037939071655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3871949017047882},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.3412981629371643},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26518377661705017},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.11720001697540283}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:figshare.com:article/14332859","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Cell_type-specific_chromatin_accessibility_analysis_in_the_mouse_and_human_brain/14332859","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.14332859","doi":"https://doi.org/10.6084/m9.figshare.14332859","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.14332859","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.14332859.v1","doi":"https://doi.org/10.6084/m9.figshare.14332859.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.14332859.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/14332859","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Cell_type-specific_chromatin_accessibility_analysis_in_the_mouse_and_human_brain/14332859","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},"sustainable_development_goals":[{"score":0.5683000087738037,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2810164974","https://openalex.org/W4387568435","https://openalex.org/W4362595446","https://openalex.org/W4410608480","https://openalex.org/W2790768464","https://openalex.org/W2750416916","https://openalex.org/W4376625797","https://openalex.org/W4283074112","https://openalex.org/W3203352734","https://openalex.org/W2979012851"],"abstract_inverted_index":{"The":[0,38],"Assay":[1],"for":[2,97],"Transposase":[3],"Accessible":[4],"Chromatin":[5],"by":[6,110,176],"sequencing":[7],"(ATAC-seq)":[8],"is":[9,19,74,172,199],"becoming":[10],"popular":[11],"in":[12,24,70,157,209,228,247],"the":[13,53,121,125,151,164,177,235,242,248],"neuroscience":[14,89],"field":[15],"where":[16],"chromatin":[17,71,99,129,169,187,206],"regulation":[18],"thought":[20],"to":[21,55,77,203,240],"be":[22],"involved":[23],"neurodevelopment,":[25],"activity-dependent":[26],"gene":[27,60],"regulation,":[28],"hormonal":[29],"and":[30,33,52,115,146,149,211,232],"environmental":[31],"responses,":[32],"pathophysiology":[34],"of":[35,40,47,59,88,127,153,168,185,237,244],"neuropsychiatric":[36],"disorders.":[37],"advantages":[39],"using":[41,136],"ATAC-seq":[42,195,224],"include":[43],"a":[44,57,64,86,103,200],"small":[45],"amount":[46],"material":[48],"needed,":[49],"fast":[50],"protocol,":[51],"ability":[54],"capture":[56,204],"range":[58,87],"regulatory":[61,155],"elements":[62,156],"with":[63,85,197],"single":[65],"assay.":[66],"With":[67],"increasing":[68],"interest":[69],"research,":[72],"it":[73],"an":[75],"imperative":[76],"have":[78],"feasible,":[79],"reliable":[80],"assays":[81],"that":[82,120,141,163,221],"are":[83],"compatible":[84],"study":[90,118,161,215,230],"designs.":[91],"Here":[92],"we":[93,139],"tested":[94],"three":[95],"protocols":[96,143],"neuronal":[98,158],"accessibility":[100,170,207],"analysis,":[101],"including":[102],"varying":[104],"brain":[105,134,192,218],"tissue":[106,135],"freezing":[107,178],"method":[108,123,202,239],"followed":[109],"fluorescence-activated":[111],"nuclei":[112],"sorting":[113],"(FANS)":[114],"ATAC-seq.":[116,137],"Our":[117,160,214],"shows":[119],"cryopreservation":[122],"impacts":[124],"number":[126],"open":[128],"regions":[130],"identified":[131],"from":[132],"frozen":[133],"However,":[138],"show":[140],"all":[142],"generate":[144,222],"consistent":[145],"robust":[147],"data":[148,171,225],"enable":[150],"identification":[152],"functional":[154],"cells.":[159],"implies":[162],"broad":[165],"biological":[166],"interpretation":[167],"not":[173],"significantly":[174],"affected":[175],"condition.":[179],"We":[180],"also":[181],"reveal":[182],"additional":[183],"challenges":[184],"doing":[186],"analysis":[188],"on":[189],"post-mortem":[190],"human":[191,212],"tissue.":[193],"Overall,":[194],"coupled":[196],"FANS":[198],"powerful":[201],"cell-type-specific":[205],"information":[208],"mouse":[210],"brain.":[213,249],"provides":[216],"alternative":[217],"preservation":[219],"methods":[220],"high-quality":[223],"while":[226],"fitting":[227],"different":[229],"designs,":[231],"further":[233],"encourages":[234],"use":[236],"this":[238],"uncover":[241],"role":[243],"epigenetic":[245],"(dys)regulation":[246]},"counts_by_year":[],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2024-04-08T00:00:00"}