How to Use the Atlas
The Canine Atlas consists of a collection of pages with photographs, tables, and text describing the data. A general text search function will enable pages to be quickly located. The sections are broken down by:
A photo gallery showing development of several organs at each Canis familiaris developmental stage (CfS) is found in the Stage Pages.
A photo gallery showing organ development through all developmental stages available is found in the Organ Pages. These are viewed by organ: Whole embryo, Forelimb & Hindlimb, Heart, Lungs, Head, Eye, Liver, Kidney, and Urogenital System.
Classification criteria for each CfS are in two tables:
Quick Reference Comparison Table and Comprehensive Comparison Table of Stages, in the TABLES section. The Comprehensive Comparison Table compares text of the CfS criteria to those for the mouse (Theiler Stages, TS) and the human (Carnegie Stages, CS), based on published information (see References). The Quick Reference Comparison Table is designed for quick correlation of CfS, TS, and CS, and does not contain text explaining classification criteria. For quick reference, this table can also be accessed by clicking the “Species Comparison Table” in the upper right corner from all Stage and Organ pages.
The Embryo Pedigree Information Table provides an overview of animals and includes information such as ID#, litter#, gestational age, CfS, crown rump length, sex, and breed for each animal. Genomic DNA samples from some embryos have been deposited in the Cornell Veterinary BioBank, where they can be accessed using the embryo ID#. The pedigree information can help researchers identify related individuals for potential use in GWAS or linkage analysis.
The Gestation Timing Information Table contains the actual data used to calculate gestational age for Canine Atlas embryos. Gestation was timed by serial measurement of the dam’s serum progesterone (P4) to estimate the day of the luteinizing hormone (LH) surge prior to ovulation.
The RNA-seq Organs by Stage Table lists information, such as ID#, gestational age, and CfS for the embryonic organs from which published RNA data are publicly available. In addition, there is an RNA-Sequenced label adjacent to photos when RNA data is available for that organ at that stage. In the urogenital system, clicking on this button will lead the visitor to a URL where the sequence data is deposited. For all other organs, this function will be added in the future, when the data has been deposited in a publicly accessible database.
Long Term Considerations:
The Canine Atlas is the first step toward developing a general repository for canine genomics that includes mutant model information and access to canine samples, similar to the Mouse Genome Informatics website (http://informatics.jax.org). Eventually, we expect that researchers will be able to access the genome sequence, phenotype, and transcriptomes from mutant models and controls, including those in the Canine Atlas, for expression quantitative trait loci (e-QTL) comparisons. As the Cornell Veterinary BioBank grows and attracts more investigators interested in using canine models to study inherited canine and human disorders, we envision the Canine Atlas will be modified to incorporate additional phenotypes and genotypes, and will allow researchers to compare normal and mutant canine genotypes and phenotypes. The Cornell College of Veterinary Medicine is the ideal environment for this resource, as we have several clinicians and researchers actively participating in the Vertebrate Genomics and Canine Genomics Research Groups and the Veterinary BioBank containing samples from clinically normal and mutant canine phenotypes.
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