{"id":65,"date":"2023-01-31T20:53:28","date_gmt":"2023-01-31T20:53:28","guid":{"rendered":"https:\/\/supervised-morphogenesis.eu\/?page_id=65"},"modified":"2026-08-28T14:07:00","modified_gmt":"2026-08-28T14:07:00","slug":"protocols","status":"publish","type":"page","link":"https:\/\/supervised-morphogenesis.eu\/index.php\/protocols\/","title":{"rendered":"Protocols"},"content":{"rendered":"\n

To maximize the reproducibility of stem-cell-based embryo models across laboratories, SUMO is committed to sharing detailed protocols.<\/p>\n\n\n\n

Co-aggregation protocol<\/h3>\n\n\n\n

Modular aggregoid strategy that spatially couples embryonic and extraembryonic endoderm-like cells to reconstruct key interactions in vitro<\/em>.<\/p>\n\n\n\n

https:\/\/doi.org\/10.1101\/2025.11.09.687163<\/a><\/p>\n\n\n\n

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Schematic overview of the co-aggregation protocol<\/em><\/figcaption><\/figure>\n\n\n\n
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Protocol for the Design and Fabrication of the rOoC Platform<\/h3>\n\n\n\n

The rOoC platform comprises a pump-free, directional-flow recirculating organ-on-a-chip (rOoC) system that generates controlled, unidirectional, gravity-driven flow through the integration of a 3D tilting mechanism and an optimized microfluidic layout.<\/p>\n\n\n\n

The platform enables the cultivation and interconnection of two or more tissue or organ representations on-chip, while allowing the incorporation of concentration gradients, endothelial barriers, microvasculature, and circulating cells. These features are integrated within the chip, eliminating the need for external tubing and auxiliary support systems.<\/p>\n\n\n\n

https:\/\/doi.org\/10.1039\/d2lc00919f<\/a><\/p>\n\n\n\n

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Platform layout<\/em><\/figcaption><\/figure>\n\n\n\n
\n\n\n\n

To generate more in-depth understanding of Raman chemical signalling, we have developed an autoencoder which predicts biochemical maps within tissues.<\/h3>\n\n\n\n

A detailed step-by-step protocol how to run RamanSpy and the Autoencoder can be found here:
https:\/\/www.science.org\/doi\/10.1126\/sciadv.aec5080<\/a>
https:\/\/github.com\/barahona-research-group\/dl-raman<\/a><\/p>\n\n\n\n

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Schematic overview<\/em> of the protocol<\/em><\/figcaption><\/figure>\n\n\n\n
\n\n\n\n

Protocol for generation of trunk-like-structures (& gastruloids)<\/h3>\n\n\n\n

You can find a detailed step-by-step protocol used by the Veenvliet Lab for the generation of trunk-like-structures and gastruloids (Veenvliet et al., Science 2020) here: https:\/\/en.bio-protocol.org\/en\/bpdetail?id=4042&type=0<\/a><\/p>\n\n\n\n

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Schematic overview<\/em><\/figcaption><\/figure>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

To maximize the reproducibility of stem-cell-based embryo models across laboratories, SUMO is committed to sharing detailed protocols. Co-aggregation protocol Modular aggregoid strategy that spatially couples embryonic and extraembryonic endoderm-like cells to reconstruct key interactions in vitro. https:\/\/doi.org\/10.1101\/2025.11.09.687163 Protocol for the Design and Fabrication of the rOoC Platform The rOoC platform comprises a pump-free, directional-flow recirculating […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-65","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/pages\/65","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/comments?post=65"}],"version-history":[{"count":20,"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/pages\/65\/revisions"}],"predecessor-version":[{"id":580,"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/pages\/65\/revisions\/580"}],"wp:attachment":[{"href":"https:\/\/supervised-morphogenesis.eu\/index.php\/wp-json\/wp\/v2\/media?parent=65"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}