[{"file":[{"success":1,"date_created":"2026-07-23T06:33:24Z","access_level":"open_access","file_size":5531906,"checksum":"cf04b061a48548a649e6a2435bf120db","date_updated":"2026-07-23T06:33:24Z","file_id":"22389","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2026_StarProtocols_Kobayashi.pdf"}],"OA_type":"gold","title":"Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination","DOAJ_listed":"1","external_id":{"pmid":["41455105"]},"article_number":"104295","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"20","citation":{"mla":"Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>, vol. 7, no. 1, 104295, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>.","apa":"Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana, K. (2026). Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>","chicago":"Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.” <i>STAR Protocols</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">https://doi.org/10.1016/j.xpro.2025.104295</a>.","ama":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. 2026;7(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2025.104295\">10.1016/j.xpro.2025.104295</a>","ista":"Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2026. Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7(1), 104295.","ieee":"W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana, “Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination,” <i>STAR Protocols</i>, vol. 7, no. 1. Elsevier, 2026.","short":"W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana, STAR Protocols 7 (2026)."},"year":"2026","publisher":"Elsevier","project":[{"_id":"9136c684-16d5-11f0-9cad-91c0177b365f","name":"Circadian structural transitions of chromatin","grant_number":"101162145"}],"supplementarymaterial":"yes","file_date_updated":"2026-07-23T06:33:24Z","article_processing_charge":"Yes","intvolume":"         7","abstract":[{"lang":"eng","text":"Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.\r\nFor complete details on the use and execution of this protocol, please refer to Michael et al.1"}],"das_tickbox":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2666-1667"]},"date_published":"2026-03-20T00:00:00Z","publication":"STAR Protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"yes","status":"public","oa_version":"Published Version","month":"03","oa":1,"type":"journal_article","has_accepted_license":"1","issue":"1","date_updated":"2026-07-23T06:34:37Z","volume":7,"date_created":"2026-01-04T23:01:33Z","PlanS_conform":"1","dataavailabilitystatement":"Raw SeEN-seq data of ESRRB nucleosome binding have been deposited on the Sequence Read Achieve database under the accession PRJNA1305216. Example analysis scripts and input files for SeEN-seq analysis can be found at https://doi.org/10.5281/zenodo.17665082.","acknowledgement":"We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).","publication_status":"published","pmid":1,"doi":"10.1016/j.xpro.2025.104295","quality_controlled":"1","OA_place":"publisher","department":[{"_id":"AlMi"}],"scopus_import":"1","_id":"20924","corr_author":"1","article_type":"original","ddc":["570"],"author":[{"first_name":"Wataru","full_name":"Kobayashi, Wataru","last_name":"Kobayashi"},{"last_name":"Michael","orcid":"0000-0002-6080-839X","first_name":"Alicia","full_name":"Michael, Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"last_name":"Ruangroengkulrith","full_name":"Ruangroengkulrith, Siwat","first_name":"Siwat"},{"full_name":"Kümmecke, Maximilian","first_name":"Maximilian","last_name":"Kümmecke"},{"first_name":"Kikuë","full_name":"Tachibana, Kikuë","last_name":"Tachibana"}]},{"abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2666-1667"]},"date_published":"2024-03-15T00:00:00Z","file":[{"date_created":"2024-07-16T12:04:46Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2024_STARProtoc_Hansen.pdf","relation":"main_file","creator":"dernst","date_updated":"2024-07-16T12:04:46Z","checksum":"4644d537451c5c114a9d7c7829b65bba","file_size":3758943,"file_id":"17264"}],"title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","external_id":{"pmid":["38165800"]},"article_number":"102795","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"15","citation":{"ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 5, no. 1, 102795, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>.","apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>.","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795."},"year":"2024","file_date_updated":"2024-07-16T12:04:46Z","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of radial neuronal migration","grant_number":"24812"}],"publisher":"Elsevier","article_processing_charge":"Yes","intvolume":"         5","date_created":"2024-01-14T23:00:56Z","acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","publication_status":"published","pmid":1,"doi":"10.1016/j.xpro.2023.102795","quality_controlled":"1","department":[{"_id":"SiHi"}],"scopus_import":"1","_id":"14794","corr_author":"1","article_type":"review","ddc":["570"],"related_material":{"link":[{"relation":"software","url":"http://github.com/hippenmeyerlab"}]},"author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"publication":"STAR Protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","month":"03","oa":1,"has_accepted_license":"1","type":"journal_article","issue":"1","volume":5,"date_updated":"2025-04-15T07:32:40Z"},{"date_created":"2024-06-30T22:01:04Z","pmid":1,"acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","publication_status":"published","scopus_import":"1","OA_place":"publisher","department":[{"_id":"SiHi"}],"quality_controlled":"1","doi":"10.1016/j.xpro.2024.103157","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung"},{"first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"ddc":["570"],"article_type":"original","_id":"17187","corr_author":"1","oa_version":"Published Version","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"STAR Protocols","month":"09","issue":"3","ec_funded":1,"has_accepted_license":"1","type":"journal_article","oa":1,"date_updated":"2025-12-30T10:54:11Z","volume":5,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1"}],"publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"date_published":"2024-09-20T00:00:00Z","file":[{"creator":"dernst","file_id":"18809","checksum":"d8a8cdba82a394e731aa699ace1ae433","date_updated":"2025-01-09T12:12:40Z","file_size":5186071,"content_type":"application/pdf","file_name":"2024_STARProtoc_Cheung.pdf","relation":"main_file","success":1,"access_level":"open_access","date_created":"2025-01-09T12:12:40Z"}],"OA_type":"gold","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","day":"20","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"},"article_number":"103157","external_id":{"pmid":["38935508"]},"year":"2024","citation":{"ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>"},"intvolume":"         5","article_processing_charge":"Yes","APC_amount":"804 EUR","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"publisher":"Elsevier","file_date_updated":"2025-01-09T12:12:40Z"},{"date_published":"2024-09-20T00:00:00Z","publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"intvolume":"         5","APC_amount":"804 EUR","article_processing_charge":"Yes","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"file_date_updated":"2025-01-09T12:16:53Z","publisher":"Elsevier","year":"2024","citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024)."},"day":"20","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"},"article_number":"103168","external_id":{"pmid":["38968076"]},"OA_type":"gold","file":[{"success":1,"access_level":"open_access","date_created":"2025-01-09T12:16:53Z","creator":"dernst","file_id":"18810","checksum":"464f52ecc6ec92f509552823bb82bf79","file_size":6445556,"date_updated":"2025-01-09T12:16:53Z","content_type":"application/pdf","file_name":"2024_STARProtoc_Cheung2.pdf","relation":"main_file"}],"title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"article_type":"original","ddc":["570"],"_id":"17232","corr_author":"1","scopus_import":"1","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"OA_place":"publisher","quality_controlled":"1","doi":"10.1016/j.xpro.2024.103168","pmid":1,"acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","publication_status":"published","date_created":"2024-07-14T22:01:10Z","date_updated":"2025-12-30T10:54:12Z","volume":5,"issue":"3","type":"journal_article","has_accepted_license":"1","oa":1,"month":"09","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"STAR Protocols"},{"_id":"18601","corr_author":"1","article_type":"original","ddc":["570"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19763"}]},"author":[{"full_name":"Rus, Stefanie","first_name":"Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"last_name":"Kulig","id":"3331f5ae-e896-11ec-af79-eeb79769bcb7","first_name":"Monika Aleksandra","full_name":"Kulig, Monika Aleksandra"},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","first_name":"Thomas","last_name":"Minchington"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.xpro.2024.103187","quality_controlled":"1","department":[{"_id":"AnKi"},{"_id":"NanoFab"}],"OA_place":"publisher","scopus_import":"1","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.","publication_status":"published","pmid":1,"date_created":"2024-12-01T23:01:53Z","date_updated":"2026-08-23T22:30:37Z","volume":5,"oa":1,"has_accepted_license":"1","type":"journal_article","issue":"4","month":"12","publication":"STAR Protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Published Version","date_published":"2024-12-20T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2666-1667"]},"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"}],"acknowledged_ssus":[{"_id":"NanoFab"}],"file_date_updated":"2024-12-03T10:53:23Z","project":[{"grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011"}],"publisher":"Elsevier","APC_amount":"804 EUR","article_processing_charge":"Yes","intvolume":"         5","citation":{"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.","short":"S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024).","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>.","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.","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>","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>.","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>"},"year":"2024","DOAJ_listed":"1","external_id":{"pmid":["39602310"]},"article_number":"103187","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"20","OA_type":"gold","file":[{"success":1,"access_level":"open_access","date_created":"2024-12-03T10:53:23Z","file_id":"18610","date_updated":"2024-12-03T10:53:23Z","file_size":4989169,"checksum":"0c61a6f9978608a103865905e06f4581","creator":"dernst","relation":"main_file","file_name":"2024_STARProtoc_Lehr.pdf","content_type":"application/pdf"}],"title":"Protocol for fabricating elastomeric stencils for patterned stem cell differentiation"},{"citation":{"apa":"Amberg, N., &#38; Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 2, no. 4, 100939, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>.","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>.","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 2, no. 4. Cell Press, 2021.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021)."},"year":"2021","article_processing_charge":"Yes","publisher":"Cell Press","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2021-11-22T08:23:58Z","intvolume":"         2","file":[{"file_id":"10329","date_updated":"2021-11-22T08:23:58Z","checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","file_size":7309464,"creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_name":"2021_STARProtocols_Amberg.pdf","success":1,"access_level":"open_access","date_created":"2021-11-22T08:23:58Z"}],"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","article_number":"100939","day":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2666-1667"]},"date_published":"2021-11-10T00:00:00Z","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","ec_funded":1,"type":"journal_article","oa":1,"issue":"4","volume":2,"date_updated":"2025-04-15T08:23:07Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"STAR Protocols","status":"public","oa_version":"Published Version","month":"11","doi":"10.1016/j.xpro.2021.100939","quality_controlled":"1","scopus_import":"1","department":[{"_id":"SiHi"}],"ddc":["573"],"article_type":"original","corr_author":"1","_id":"10321","author":[{"last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"date_created":"2021-11-21T23:01:28Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publication_status":"published"},{"status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"STAR Protocols","month":"12","issue":"4","ec_funded":1,"type":"journal_article","has_accepted_license":"1","oa":1,"date_updated":"2025-05-14T11:26:30Z","volume":2,"date_created":"2021-12-19T23:01:32Z","publication_status":"published","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","scopus_import":"1","department":[{"_id":"SaSi"}],"quality_controlled":"1","doi":"10.1016/j.xpro.2021.101012","author":[{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro","last_name":"Venturino"},{"last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","ddc":["573"],"_id":"10565","title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","file":[{"creator":"cchlebak","date_updated":"2021-12-20T08:58:40Z","file_size":6207060,"checksum":"9ea2501056c5df99e84726b845e9b976","file_id":"10570","content_type":"application/pdf","file_name":"2021_STARProt_Venturino.pdf","relation":"main_file","success":1,"date_created":"2021-12-20T08:58:40Z","access_level":"open_access"}],"day":"17","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_number":"101012","year":"2021","citation":{"ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” <i>STAR Protocols</i>, vol. 2, no. 4. Elsevier, 2021.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>, vol. 2, no. 4, 101012, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>.","apa":"Venturino, A., &#38; Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>.","ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>"},"intvolume":"         2","article_processing_charge":"Yes","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"publisher":"Elsevier","file_date_updated":"2021-12-20T08:58:40Z","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021)."}],"publication_identifier":{"eissn":["2666-1667"]},"language":[{"iso":"eng"}],"date_published":"2021-12-17T00:00:00Z"}]