{"id":"https://openalex.org/W4253884338","doi":"https://doi.org/10.17504/protocols.io.bur4nv8w","title":"A method to recapitulate early embryonic spatial patterning in human embryonic stem cells v1","display_name":"A method to recapitulate early embryonic spatial patterning in human embryonic stem cells v1","publication_year":2021,"publication_date":"2021-05-05","ids":{"openalex":"https://openalex.org/W4253884338","doi":"https://doi.org/10.17504/protocols.io.bur4nv8w"},"language":"en","primary_location":{"id":"doi:10.17504/protocols.io.bur4nv8w","doi":"https://doi.org/10.17504/protocols.io.bur4nv8w","is_oa":true,"landing_page_url":"https://doi.org/10.17504/protocols.io.bur4nv8w","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.17504/protocols.io.bur4nv8w","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022896439","display_name":"Aryeh Warmflash","orcid":"https://orcid.org/0000-0002-5679-2268","observed_orcids":["https://orcid.org/0000-0002-5679-2268"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aryeh Warmflash","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078646816","display_name":"Beno\u00eet Sorre","orcid":"https://orcid.org/0000-0001-8810-3298","observed_orcids":["https://orcid.org/0000-0001-8810-3298"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Benoit Sorre","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036608533","display_name":"Fred Etoc","orcid":"https://orcid.org/0000-0002-5859-2382","observed_orcids":["https://orcid.org/0000-0002-5859-2382"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fred Etoc","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036408112","display_name":"Eric D. Siggia","orcid":"https://orcid.org/0000-0001-7482-1854","observed_orcids":["https://orcid.org/0000-0001-7482-1854"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eric D. Siggia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5016600632","display_name":"Ali H. Brivanlou","orcid":"https://orcid.org/0000-0002-1761-280X","observed_orcids":["https://orcid.org/0000-0002-1761-280X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ali H. Brivanlou","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.7318999767303467,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.7318999767303467,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.2632000148296356,"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/T10608","display_name":"Neurogenesis and neuroplasticity mechanisms","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/2806","display_name":"Developmental Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/human-embryonic-stem-cells","display_name":"human embryonic stem cells","score":0.9089999794960022},{"id":"https://openalex.org/keywords/early-embryonic-patterning","display_name":"early embryonic patterning","score":0.7490000128746033},{"id":"https://openalex.org/keywords/three-germ-layers","display_name":"three germ layers","score":0.7039999961853027},{"id":"https://openalex.org/keywords/geometric-confinement","display_name":"confined geometries","score":0.8339999914169312},{"id":"https://openalex.org/keywords/bmp4-signaling","display_name":"BMP4 signaling","score":0.9430000185966492},{"id":"https://openalex.org/keywords/activin-nodal-signaling","display_name":"Activin/Nodal signaling","score":0.8669999837875366},{"id":"https://openalex.org/keywords/mesendoderm","display_name":"mesendoderm","score":0.6940000057220459},{"id":"https://openalex.org/keywords/trophectoderm","display_name":"trophectoderm","score":0.8629999756813049},{"id":"https://openalex.org/keywords/primitive-streak","display_name":"primitive streak","score":0.6230000257492065},{"id":"https://openalex.org/keywords/paracrine-signaling","display_name":"paracrine signaling","score":0.8930000066757202},{"id":"https://openalex.org/keywords/self-organization","display_name":"self-organization","score":0.6200000047683716}],"concepts":[{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.7380070686340332},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7162851095199585},{"id":"https://openalex.org/C18155467","wikidata":"https://www.wikidata.org/wiki/Q660498","display_name":"Germ layer","level":5,"score":0.6967759728431702},{"id":"https://openalex.org/C66518211","wikidata":"https://www.wikidata.org/wiki/Q247512","display_name":"Primitive streak","level":5,"score":0.6909341216087341},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.6337611675262451},{"id":"https://openalex.org/C129536746","wikidata":"https://www.wikidata.org/wiki/Q1141026","display_name":"Gastrulation","level":4,"score":0.5713759064674377},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.5019314289093018},{"id":"https://openalex.org/C7876069","wikidata":"https://www.wikidata.org/wiki/Q14873666","display_name":"Paracrine signalling","level":3,"score":0.4907172918319702},{"id":"https://openalex.org/C196843134","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryo","level":2,"score":0.36767706274986267},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.28654247522354126},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.27852481603622437},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23940598964691162},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0669809877872467},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.17504/protocols.io.bur4nv8w","doi":"https://doi.org/10.17504/protocols.io.bur4nv8w","is_oa":true,"landing_page_url":"https://doi.org/10.17504/protocols.io.bur4nv8w","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.17504/protocols.io.bur4nv8w","doi":"https://doi.org/10.17504/protocols.io.bur4nv8w","is_oa":true,"landing_page_url":"https://doi.org/10.17504/protocols.io.bur4nv8w","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"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/W1998317358","https://openalex.org/W2531559910","https://openalex.org/W7039326110","https://openalex.org/W3116475705","https://openalex.org/W2954342710","https://openalex.org/W4384559624","https://openalex.org/W3196651579","https://openalex.org/W6958863651","https://openalex.org/W2535856472","https://openalex.org/W2800459279"],"abstract_inverted_index":{"Embryos":[0],"allocate":[1],"cells":[2,16,129],"to":[3,42,50,56,79,90,105,130],"the":[4,20,80,91,100,106,124],"three":[5,21],"germ":[6,22],"layers":[7,23,93],"in":[8,24,46,73],"a":[9,66,83,111,142],"spatially":[10,32],"ordered":[11],"sequence.":[12],"Human":[13],"embryonic":[14],"stem":[15,128],"(hESCs)":[17],"can":[18,133],"generate":[19],"culture,":[25],"however,":[26],"differentiation":[27],"is":[28,40],"typically":[29],"heterogeneous":[30],"and":[31,65,109,140],"disordered.":[33],"Here":[34],"we":[35],"show":[36],"that":[37,116,123],"geometric":[38],"confinement":[39],"sufficient":[41],"trigger":[43],"self-organized":[44],"patterning":[45],"hESCs.":[47],"In":[48],"response":[49],"BMP4,":[51],"these":[52],"colonies":[53,88],"reproducibly":[54],"differentiate":[55],"an":[57,61],"outer":[58,92],"trophectoderm-like":[59],"ring,":[60],"inner":[62],"ectodermal":[63],"circle":[64],"ring":[67],"of":[68,94,102,113,127],"mesendoderm":[69],"expressing":[70],"primitive-streak":[71],"markers":[72],"between.":[74],"Fates":[75],"are":[76],"defined":[77],"relative":[78],"boundary":[81],"with":[82],"fixed":[84],"length":[85],"scale:":[86],"small":[87],"correspond":[89],"larger":[95],"ones.":[96],"Inhibitory":[97],"signals":[98],"limit":[99],"range":[101],"BMP4":[103],"signaling":[104,115],"colony":[107,138],"edge":[108],"induce":[110],"gradient":[112],"Activin/Nodal":[114],"patterns":[117,132],"mesendodermal":[118],"fates.":[119],"These":[120],"results":[121],"demonstrate":[122],"intrinsic":[125],"tendency":[126],"make":[131],"be":[134],"harnessed":[135],"by":[136],"controlling":[137],"geometries,":[139],"provide":[141],"quantitative":[143],"assay":[144],"for":[145],"studying":[146],"paracrine":[147],"signaling.":[148]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2022-05-12T00:00:00"}
