A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.
A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.
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DOI：
10.1371/journal.pcbi.1003670
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发表时间：
2014-06
影响因子：
4.3
通讯作者：
Santos A
中科院分区：
文献类型：
--
作者：
Castro-González C;Luengo-Oroz MA;Duloquin L;Savy T;Rizzi B;Desnoulez S;Doursat R;Kergosien YL;Ledesma-Carbayo MJ;Bourgine P;Peyriéras N;Santos A
基因表达图谱是量化和理解胚胎发生在时间和空间上的多尺度过程的重要资源。脊椎动物早期胚胎的原型4D图谱的自动化重建，使用荧光原位杂交与核复染，需要专门的计算策略。为了实现这一目标，我们设计了一个原始的方法框架，在一个名为Match-IT的软件工具中实现。只需最少的人工监督，我们的系统就能够收集在不同分析胚胎中观察到的具有表型变异性的基因表达模式，并将它们随时间推移映射到一系列常见的3D模板上，创建4D图谱。该框架用于构建由来自一组斑马鱼早期胚胎的6个基因表达模板组成的图谱，所述斑马鱼早期胚胎跨越从4至6.3 hpf（受精后小时）的6个发育阶段。他们包括53个标本，181，415个检测到的细胞核，以及在3D中观察到的9个不同基因的98个基因表达模式的分割。此外，还开发了一个交互式可视化软件，即MSPAS-IT，以检查、监督和分析地图集。Match-IT和Matchas-IT，包括用户手册、代表性数据集和视频教程，可在网上免费公开获取。我们还提出了计算方法和工具，在细胞尺度上的基因表达模板的定量评估，共表达模式的识别，可视化和分析，synexpression组和它们的动态通过发育阶段。我们提出了一个工作流程，映射到一系列的3D模板，或“图集”，在早期胚胎发生多个基因的表达域。将其应用于4和6.3 hpf之间的不同阶段的斑马鱼，产生6个模板。我们的系统克服了缺乏显着的形态标志，在早期发展依赖于一个参考基因（goosecoid，gsc）的表达和核染色，以指导注册的分析基因。所提出的方法还成功地从部分成像的胚胎中映射基因结构域，从而允许更大的显微镜放大倍数和细胞分辨率。利用该工作流构建了斑马鱼时空数据库，为脊椎动物胚胎发生的系统分析开辟了道路。地图集数据库、绘图软件（Match-IT）、定制的可视化平台（Matchas-IT）和逐步用户指南可在补充材料中查阅。我们希望这将鼓励其他实验室生成，绘制，可视化和分析新的基因表达数据集。
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages. We propose a workflow to map the expression domains of multiple genes onto a series of 3D templates, or “atlas”, during early embryogenesis. It was applied to the zebrafish at different stages between 4 and 6.3 hpf, generating 6 templates. Our system overcomes the lack of significant morphological landmarks in early development by relying on the expression of a reference gene (goosecoid, gsc) and nuclear staining to guide the registration of the analyzed genes. The proposed method also successfully maps gene domains from partially imaged embryos, thus allowing greater microscope magnification and cellular resolution. By using the workflow to construct a spatiotemporal database of zebrafish, we opened the way to a systematic analysis of vertebrate embryogenesis. The atlas database, together with the mapping software (Match-IT), a custom-made visualization platform (Atlas-IT), and step-by-step user guides are available from the Supplementary Material. We expect that this will encourage other laboratories to generate, map, visualize and analyze new gene expression datasets.
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影响因子：
10.9
作者：
Maintz, J B;Viergever, M A
通讯作者：
Viergever, M A
影响因子：
4.3
作者：
Crombach A;Wotton KR;Cicin-Sain D;Ashyraliyev M;Jaeger J
通讯作者：
Jaeger J
影响因子：
2.7
作者：
Fisher, Malcolm E.;Clelland, Allyson K.;Bain, Andrew;Baldock, Richard A.;Murphy, Paula;Downie, Helen;Tickle, Cheryll;Davidson, Duncan R.;Buckland, Richard A.
通讯作者：
Buckland, Richard A.
DOI：
10.3791/1229
发表时间：
2009-03-25
期刊：
Journal of visualized experiments : JoVE
影响因子：
--
作者：
Brend, Tim;Holley, Scott A
通讯作者：
Holley, Scott A
影响因子：
1
作者：
DUNCAN, T;PHILLIPS, RB;WAGNER, WH
通讯作者：
WAGNER, WH