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Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space

Increased information on the encoded mammalian genome is expected to facilitate an integrated understanding of complex anatomical structure and function based on the knowledge of gene products. Determination of gene expression-anatomy associations is crucial for this understanding. To elicit the ass...

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Autores principales: Okamura-Oho, Yuko, Shimokawa, Kazuro, Takemoto, Satoko, Hirakiyama, Asami, Nakamura, Sakiko, Tsujimura, Yuki, Nishimura, Masaomi, Kasukawa, Takeya, Masumoto, Koh-hei, Nikaido, Itoshi, Shigeyoshi, Yasufumi, Ueda, Hiroki R., Song, Gang, Gee, James, Himeno, Ryutaro, Yokota, Hideo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446890/
https://www.ncbi.nlm.nih.gov/pubmed/23028969
http://dx.doi.org/10.1371/journal.pone.0045373
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author Okamura-Oho, Yuko
Shimokawa, Kazuro
Takemoto, Satoko
Hirakiyama, Asami
Nakamura, Sakiko
Tsujimura, Yuki
Nishimura, Masaomi
Kasukawa, Takeya
Masumoto, Koh-hei
Nikaido, Itoshi
Shigeyoshi, Yasufumi
Ueda, Hiroki R.
Song, Gang
Gee, James
Himeno, Ryutaro
Yokota, Hideo
author_facet Okamura-Oho, Yuko
Shimokawa, Kazuro
Takemoto, Satoko
Hirakiyama, Asami
Nakamura, Sakiko
Tsujimura, Yuki
Nishimura, Masaomi
Kasukawa, Takeya
Masumoto, Koh-hei
Nikaido, Itoshi
Shigeyoshi, Yasufumi
Ueda, Hiroki R.
Song, Gang
Gee, James
Himeno, Ryutaro
Yokota, Hideo
author_sort Okamura-Oho, Yuko
collection PubMed
description Increased information on the encoded mammalian genome is expected to facilitate an integrated understanding of complex anatomical structure and function based on the knowledge of gene products. Determination of gene expression-anatomy associations is crucial for this understanding. To elicit the association in the three-dimensional (3D) space, we introduce a novel technique for comprehensive mapping of endogenous gene expression into a web-accessible standard space: Transcriptome Tomography. The technique is based on conjugation of sequential tissue-block sectioning, all fractions of which are used for molecular measurements of gene expression densities, and the block- face imaging, which are used for 3D reconstruction of the fractions. To generate a 3D map, tissues are serially sectioned in each of three orthogonal planes and the expression density data are mapped using a tomographic technique. This rapid and unbiased mapping technique using a relatively small number of original data points allows researchers to create their own expression maps in the broad anatomical context of the space. In the first instance we generated a dataset of 36,000 maps, reconstructed from data of 61 fractions measured with microarray, covering the whole mouse brain (ViBrism: http://vibrism.riken.jp/3dviewer/ex/index.html) in one month. After computational estimation of the mapping accuracy we validated the dataset against existing data with respect to the expression location and density. To demonstrate the relevance of the framework, we showed disease related expression of Huntington’s disease gene and Bdnf. Our tomographic approach is applicable to analysis of any biological molecules derived from frozen tissues, organs and whole embryos, and the maps are spatially isotropic and well suited to the analysis in the standard space (e.g. Waxholm Space for brain-atlas databases). This will facilitate research creating and using open-standards for a molecular-based understanding of complex structures; and will contribute to new insights into a broad range of biological and medical questions.
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spelling pubmed-34468902012-10-01 Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space Okamura-Oho, Yuko Shimokawa, Kazuro Takemoto, Satoko Hirakiyama, Asami Nakamura, Sakiko Tsujimura, Yuki Nishimura, Masaomi Kasukawa, Takeya Masumoto, Koh-hei Nikaido, Itoshi Shigeyoshi, Yasufumi Ueda, Hiroki R. Song, Gang Gee, James Himeno, Ryutaro Yokota, Hideo PLoS One Research Article Increased information on the encoded mammalian genome is expected to facilitate an integrated understanding of complex anatomical structure and function based on the knowledge of gene products. Determination of gene expression-anatomy associations is crucial for this understanding. To elicit the association in the three-dimensional (3D) space, we introduce a novel technique for comprehensive mapping of endogenous gene expression into a web-accessible standard space: Transcriptome Tomography. The technique is based on conjugation of sequential tissue-block sectioning, all fractions of which are used for molecular measurements of gene expression densities, and the block- face imaging, which are used for 3D reconstruction of the fractions. To generate a 3D map, tissues are serially sectioned in each of three orthogonal planes and the expression density data are mapped using a tomographic technique. This rapid and unbiased mapping technique using a relatively small number of original data points allows researchers to create their own expression maps in the broad anatomical context of the space. In the first instance we generated a dataset of 36,000 maps, reconstructed from data of 61 fractions measured with microarray, covering the whole mouse brain (ViBrism: http://vibrism.riken.jp/3dviewer/ex/index.html) in one month. After computational estimation of the mapping accuracy we validated the dataset against existing data with respect to the expression location and density. To demonstrate the relevance of the framework, we showed disease related expression of Huntington’s disease gene and Bdnf. Our tomographic approach is applicable to analysis of any biological molecules derived from frozen tissues, organs and whole embryos, and the maps are spatially isotropic and well suited to the analysis in the standard space (e.g. Waxholm Space for brain-atlas databases). This will facilitate research creating and using open-standards for a molecular-based understanding of complex structures; and will contribute to new insights into a broad range of biological and medical questions. Public Library of Science 2012-09-19 /pmc/articles/PMC3446890/ /pubmed/23028969 http://dx.doi.org/10.1371/journal.pone.0045373 Text en © 2012 Okamura-Oho et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Okamura-Oho, Yuko
Shimokawa, Kazuro
Takemoto, Satoko
Hirakiyama, Asami
Nakamura, Sakiko
Tsujimura, Yuki
Nishimura, Masaomi
Kasukawa, Takeya
Masumoto, Koh-hei
Nikaido, Itoshi
Shigeyoshi, Yasufumi
Ueda, Hiroki R.
Song, Gang
Gee, James
Himeno, Ryutaro
Yokota, Hideo
Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title_full Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title_fullStr Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title_full_unstemmed Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title_short Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
title_sort transcriptome tomography for brain analysis in the web-accessible anatomical space
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446890/
https://www.ncbi.nlm.nih.gov/pubmed/23028969
http://dx.doi.org/10.1371/journal.pone.0045373
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