| アイテムタイプ |
学術雑誌論文 / Journal Article(1) |
| 公開日 |
2025-06-26 |
| タイトル |
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タイトル |
Machine learning-based estimation of spatial gene expression pattern during ESC-derived retinal organoid development |
| 言語 |
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言語 |
eng |
| 資源タイプ |
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資源タイプ |
journal article |
| アクセス権 |
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アクセス権 |
open access |
| 著者 |
藤村, 友貴
Sakai, Itsuki
Shioka, Itsuki
Takata, Nozomu
Hashimoto, Atsushi
舩冨, 卓哉
Okuda, Satoru
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| 抄録 |
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内容記述タイプ |
Abstract |
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内容記述 |
Organoids, which can reproduce the complex tissue structures found in embryos, are revolutionizing basic research and regenerative medicine. In order to use organoids for research and medicine, it is necessary to assess the composition and arrangement of cell types within the organoid, i.e., spatial gene expression. However, current methods are invasive and require gene editing and immunostaining. In this study, we developed a non-invasive estimation method of spatial gene expression patterns using machine learning. A deep learning model with an encoder-decoder architecture was trained on paired datasets of phase-contrast and fluorescence images, and was applied to a retinal organoid derived from mouse embryonic stem cells, focusing on the master gene Rax (also called Rx), crucial for eye field development. This method successfully estimated spatially plausible fluorescent patterns with appropriate intensities, enabling the non-invasive, quantitative estimation of spatial gene expression patterns within each tissue. Thus, this method could lead to new avenues for evaluating spatial gene expression patterns across a wide range of biology and medicine fields. |
| 書誌情報 |
en : Scientific Reports
巻 13,
号 1,
発行日 2023-12-20
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| 出版者 |
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出版者 |
Nature Research |
| ISSN |
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収録物識別子タイプ |
EISSN |
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収録物識別子 |
2045-2322 |
| 出版者版DOI |
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関連タイプ |
isReplacedBy |
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識別子タイプ |
DOI |
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関連識別子 |
https://doi.org/10.1038/s41598-023-49758-y |
| 出版者版URI |
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関連タイプ |
isReplacedBy |
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識別子タイプ |
URI |
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関連識別子 |
https://www.nature.com/articles/s41598-023-49758-y |
| 権利 |
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権利情報Resource |
https://creativecommons.org/licenses/by/4.0/ |
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権利情報 |
$00A9 The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
| 著者版フラグ |
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出版タイプ |
NA |
| 助成情報 |
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助成機関名 |
Japan Science and Technology Agency(JST) |
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研究課題番号 |
JPMJCR1921 |
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研究課題名 |
力学場と生化学場の相互作用の計測・操作と予測 |
| 助成情報 |
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助成機関名 |
Japan Science and Technology Agency(JST) |
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研究課題番号 |
JPMJCR23N3 |
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研究課題名 |
マルチモーダル時空間統合オミクス解析による哺乳類細胞運命制御基盤の理解 |
| 助成情報 |
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助成機関名 |
Japan Science and Technology Agency(JST) |
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研究課題番号 |
JPMJPR2025 |
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研究課題名 |
乗法群スパースモデリングによる幾何変換場のモデル化 |
| 助成情報 |
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助成機関名 |
Japan Agency for Medical Research
and Development (AMED) |
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研究課題番号 |
21bm0704065h0003 |
| 助成情報 |
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助成機関名 |
Japan Society for the Promotion of Science (JSPS) |
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研究課題番号 |
21H01209 |
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研究課題名 |
三次元多細胞組織のアクティブな機械特性とその適応的な制御機構の解明 |
| 助成情報 |
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助成機関名 |
Japan Society for the Promotion of Science (JSPS) |
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研究課題番号 |
21KK0134 |
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研究課題名 |
タンパク工学を用いた老化におけるシナプス周囲コラーゲンの役割の解明 |
| 助成情報 |
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助成機関名 |
Japan Society for the Promotion of Science (JSPS) |
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研究課題番号 |
22K18749 |
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研究課題名 |
器官形成における組織弾塑性の適応的な制御機構と内部構造ゆらぎの役割 |
| 助成情報 |
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助成機関名 |
Japan Society for the Promotion of Science (JSPS) |
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研究課題番号 |
22H05170 |
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研究課題名 |
メカノケミカルフィードバックによる自律的秩序化原理の理論展開 |
| 助成情報 |
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助成機関名 |
Ministry of Education, Culture, Sports, Science and Technology (MEXT) |
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研究課題名 |
World
Premier International Research Center Initiative |
