[{"page":"129","oa":1,"citation":{"ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>.","short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025.","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>."},"related_material":{"record":[{"id":"18601","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17148","status":"public"},{"id":"18807","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13136","status":"public"}]},"type":"dissertation","month":"05","_id":"19763","degree_awarded":"PhD","abstract":[{"text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"date_updated":"2026-04-14T09:50:53Z","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","corr_author":"1","author":[{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093","first_name":"Stefanie","full_name":"Rus, Stefanie"}],"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","date_created":"2025-05-30T09:14:58Z","file":[{"date_updated":"2025-11-30T23:30:02Z","embargo":"2025-11-30","relation":"main_file","checksum":"8cd7fe3ca990adbcafdece119aa0973d","content_type":"application/pdf","access_level":"open_access","file_id":"19764","file_name":"Thesis_Lehr_PDFA.pdf","creator":"cchlebak","date_created":"2025-05-30T09:10:22Z","file_size":42879974},{"file_name":"Thesis_Lehr_emptyPages.docx","file_id":"19765","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"0c87dd5fc803450a47b20736b5f86a2f","relation":"source_file","date_updated":"2025-11-30T23:30:02Z","embargo_to":"open_access","file_size":18731094,"date_created":"2025-05-30T09:31:15Z","creator":"cchlebak"}],"date_published":"2025-05-29T00:00:00Z","project":[{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011"}],"year":"2025","acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","doi":"10.15479/AT-ISTA-19763","ddc":["570"],"publication_status":"published","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"day":"29","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","status":"public","supervisor":[{"first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"}],"file_date_updated":"2025-11-30T23:30:02Z"},{"oa_version":"Published Version","corr_author":"1","publisher":"Elsevier","quality_controlled":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-06-20T22:31:01Z","OA_place":"publisher","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"lang":"eng","text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues."}],"_id":"18807","related_material":{"record":[{"relation":"dissertation_contains","id":"19763","status":"public"}]},"citation":{"ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Elsevier, pp. 567–580, 2025.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>"},"type":"journal_article","month":"02","page":"567-580","oa":1,"OA_type":"hybrid","file_date_updated":"2025-04-16T10:54:07Z","has_accepted_license":"1","isi":1,"status":"public","publication_identifier":{"issn":["1534-5807"]},"day":"24","article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"publication_status":"published","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"intvolume":"        60","acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","doi":"10.1016/j.devcel.2024.10.024","ddc":["570"],"volume":60,"pmid":1,"scopus_import":"1","year":"2025","publication":"Developmental Cell","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"article_type":"original","date_published":"2025-02-24T00:00:00Z","issue":"4","file":[{"file_name":"2025_DevelopmentalCell_Lehr.pdf","relation":"main_file","date_updated":"2025-04-16T10:54:07Z","file_id":"19584","access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"bb58db4a908a1f4aabe4004706154541","file_size":6994499,"creator":"dernst","date_created":"2025-04-16T10:54:07Z"}],"date_created":"2025-01-09T11:25:47Z","author":[{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093","first_name":"Stefanie","full_name":"Rus, Stefanie"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"},{"last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas","full_name":"Minchington, Thomas"},{"id":"48A59534-F248-11E8-B48F-1D18A9856A87","last_name":"Greunz","first_name":"Martina","full_name":"Greunz, Martina"},{"first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B"},{"full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling"},{"language":[{"iso":"eng"}],"date_updated":"2026-06-20T22:31:01Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","quality_controlled":"1","publisher":"Elsevier","related_material":{"record":[{"status":"public","id":"19763","relation":"dissertation_contains"}]},"month":"08","type":"journal_article","citation":{"ieee":"T. Krammer <i>et al.</i>, “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” <i>Developmental Cell</i>, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024.","mla":"Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>.","short":"T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10.","apa":"Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>","ama":"Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. <i>Developmental Cell</i>. 2024;59(15):1940-1953.e10. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">10.1016/j.devcel.2024.04.021</a>","chicago":"Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.04.021\">https://doi.org/10.1016/j.devcel.2024.04.021</a>.","ista":"Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10."},"oa":1,"page":"1940-1953.e10","abstract":[{"lang":"eng","text":"During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering."}],"_id":"17148","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"AnKi"}],"external_id":{"isi":["001289684800001"],"pmid":["38776925"]},"publication_status":"published","status":"public","has_accepted_license":"1","isi":1,"day":"01","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"file_date_updated":"2025-01-13T10:59:12Z","OA_type":"hybrid","file":[{"creator":"dernst","date_created":"2025-01-13T10:59:12Z","file_size":6249076,"date_updated":"2025-01-13T10:59:12Z","relation":"main_file","checksum":"fefdea9c02862b4bb74de49b65ce638a","content_type":"application/pdf","success":1,"access_level":"open_access","file_id":"18841","file_name":"2024_DevelopmentalCell_Krammer.pdf"}],"issue":"15","title":"Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition","author":[{"last_name":"Krammer","first_name":"Teresa","full_name":"Krammer, Teresa"},{"first_name":"Hannah T.","full_name":"Stuart, Hannah T.","last_name":"Stuart"},{"first_name":"Elena","full_name":"Gromberg, Elena","last_name":"Gromberg"},{"last_name":"Ishihara","first_name":"Keisuke","full_name":"Ishihara, Keisuke"},{"full_name":"Cislo, Dillon","first_name":"Dillon","last_name":"Cislo"},{"first_name":"Manuela","full_name":"Melchionda, Manuela","last_name":"Melchionda"},{"first_name":"Fernando","full_name":"Becerril Perez, Fernando","last_name":"Becerril Perez"},{"full_name":"Wang, Jingkui","first_name":"Jingkui","last_name":"Wang"},{"last_name":"Costantini","first_name":"Elena","full_name":"Costantini, Elena"},{"first_name":"Stefanie","full_name":"Rus, Stefanie","last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093"},{"last_name":"Arbanas","full_name":"Arbanas, Laura","first_name":"Laura"},{"first_name":"Alexandra","full_name":"Hörmann, Alexandra","last_name":"Hörmann"},{"first_name":"Ralph A.","full_name":"Neumüller, Ralph A.","last_name":"Neumüller"},{"full_name":"Elvassore, Nicola","first_name":"Nicola","last_name":"Elvassore"},{"last_name":"Siggia","first_name":"Eric","full_name":"Siggia, Eric"},{"last_name":"Briscoe","full_name":"Briscoe, James","first_name":"James"},{"full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"},{"full_name":"Tanaka, Elly M.","first_name":"Elly M.","last_name":"Tanaka"}],"date_created":"2024-06-16T22:01:07Z","article_type":"original","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"date_published":"2024-08-01T00:00:00Z","volume":59,"publication":"Developmental Cell","year":"2024","scopus_import":"1","pmid":1,"intvolume":"        59","ddc":["570"],"doi":"10.1016/j.devcel.2024.04.021","acknowledgement":"We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission."},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2026-06-20T22:31:01Z","oa_version":"Published Version","corr_author":"1","publisher":"Elsevier","quality_controlled":"1","acknowledged_ssus":[{"_id":"NanoFab"}],"APC_amount":"804 EUR","DOAJ_listed":"1","OA_place":"publisher","month":"12","type":"journal_article","citation":{"apa":"Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","ama":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>. 2024;5(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>","ista":"Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187.","chicago":"Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">https://doi.org/10.1016/j.xpro.2024.103187</a>.","mla":"Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103187\">10.1016/j.xpro.2024.103187</a>.","ieee":"S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024."},"related_material":{"record":[{"relation":"dissertation_contains","id":"19763","status":"public"}]},"oa":1,"abstract":[{"text":"Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1","lang":"eng"}],"_id":"18601","file_date_updated":"2024-12-03T10:53:23Z","OA_type":"gold","article_processing_charge":"Yes","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","external_id":{"pmid":["39602310"]},"has_accepted_license":"1","status":"public","day":"20","publication_identifier":{"eissn":["2666-1667"]},"volume":5,"scopus_import":"1","pmid":1,"publication":"STAR Protocols","year":"2024","intvolume":"         5","doi":"10.1016/j.xpro.2024.103187","acknowledgement":"We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","ddc":["570"],"issue":"4","file":[{"date_created":"2024-12-03T10:53:23Z","creator":"dernst","file_size":4989169,"file_id":"18610","success":1,"access_level":"open_access","checksum":"0c61a6f9978608a103865905e06f4581","content_type":"application/pdf","relation":"main_file","date_updated":"2024-12-03T10:53:23Z","file_name":"2024_STARProtoc_Lehr.pdf"}],"date_created":"2024-12-01T23:01:53Z","title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation","author":[{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","full_name":"Rus, Stefanie","first_name":"Stefanie"},{"full_name":"Merrin, Jack","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","last_name":"Kulig","first_name":"Monika Aleksandra","full_name":"Kulig, Monika Aleksandra"},{"full_name":"Minchington, Thomas","first_name":"Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"first_name":"Anna","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998"}],"article_number":"103187","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"article_type":"original","date_published":"2024-12-20T00:00:00Z"},{"quality_controlled":"1","publisher":"Elsevier","corr_author":"1","oa_version":"Published Version","date_updated":"2026-06-20T22:31:01Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"_id":"13136","abstract":[{"lang":"eng","text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question."}],"oa":1,"citation":{"mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>, vol. 35, 100459, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” <i>Current Opinion in Systems Biology</i>, vol. 35. Elsevier, 2023.","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","apa":"Minchington, T., Rus, S., &#38; Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” <i>Current Opinion in Systems Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">https://doi.org/10.1016/j.coisb.2023.100459</a>.","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. <i>Current Opinion in Systems Biology</i>. 2023;35. doi:<a href=\"https://doi.org/10.1016/j.coisb.2023.100459\">10.1016/j.coisb.2023.100459</a>"},"related_material":{"record":[{"relation":"dissertation_contains","id":"19763","status":"public"}]},"month":"09","type":"journal_article","publication_identifier":{"eissn":["2452-3100"]},"day":"01","status":"public","has_accepted_license":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnKi"}],"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-01-29T11:06:45Z","date_published":"2023-09-01T00:00:00Z","article_type":"original","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"article_number":"100459","author":[{"first_name":"Thomas","full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington"},{"full_name":"Rus, Stefanie","first_name":"Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"}],"date_created":"2023-06-18T22:00:46Z","title":"Control of tissue dimensions in the developing neural tube and somites","file":[{"file_size":598842,"date_created":"2024-01-29T11:06:45Z","creator":"dernst","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","content_type":"application/pdf","checksum":"8a75c4e29fd9b62e3c50663c2265b173","access_level":"open_access","file_id":"14896","success":1,"date_updated":"2024-01-29T11:06:45Z","relation":"main_file"}],"ddc":["570"],"doi":"10.1016/j.coisb.2023.100459","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","intvolume":"        35","year":"2023","publication":"Current Opinion in Systems Biology","scopus_import":"1","volume":35}]