3D Gene Expression

Expression Atlases
Search PointClouds
Browse PointClouds
Data Releases

Overview:
   Summary
   Project Goals

Methods:
   Staining & Mounting
   Probe Constructs
   Staging
   Imaging

Software:
   PointCloudXplore
   PointCloudToolBox
   PointCloudAlign
   NODE

File Formats:
   PointCloud (.pce)
   VirtualEmbryo (.vpc)
   Correspondence files

Summary

This database allows search and retrieval of three file types describing gene expression and embryo morphology in 3D at cellular resolution: Each PointCloud file describes data from an individual embryo, typically the expression of two genes; Each VirtualEmbryo file describes average data for many genes, embryos, and developmental stages; And each Correspondence file describes the best correspondence between each cell in a PointCloud and cell(s) in the associated VirtualEmbryo. Each species or genetic variant has its own VirtualEmbryo file describing it. The collection of PointCloud and Correspondence Files and their associated VirtualEmbryo are together termed an Expression Atlas. An analysis tool, PointCloudXplore, allows visualization and analysis of the data in any of these files. Meta-data associated with each PointCloud is also provided, including detailed information on embryo collection, staining, imaging, gene probes and antibodies used, protocols, and quality estimators.

The data are produced as follows: Embryos are collected at the desired developmental stage, fixed, and fluorescently stained to label nuclei and the protein or mRNA expression patterns of several genes, each labeled in a different color. The developmental stage of embryos is judged under phase contrast microscopy. Multi-photon confocal microscopy is used to collect a 3D image stack of each labeled embryo. Automated image analysis methods then determine the location and extent of each nuclei. This information is used to generate PointCloud files that contain geometric data for each nucleus (position, volume, etc.), and the measured levels of gene expression in a single embryo (Luengo et al, 2006). To allow comparison between the expression patterns of more than two or three genes, and at multiple developmental stages, registration methods are used to place gene expression data from many embryos into a VirtualEmbryo file (Fowlkes et al, 2008).

Currently, our project's goals are focused on the gene expression network regulated by 37 principal transcription factors in the pregastrula embryo. The Expression Atlases page lists available VirtualEmbryos, summaries of average expression patterns in each and links to their constituent PointCloud and Correspondence Files. A Browse PointClouds page allows you to browse all of the available PointClouds through a summary for given genes, developmental stages, genotypes and species. The Search PointCloud page allows selection of user defined subsets of PointClouds and their associated meta-data. A description of the current and past data releases of our datasets is available. Previous releases may be downloaded from there.

Note that because of their large size (300 - 500 Mb) the original 3D confocal image stack files are not available from this public database, but are available by request.