Towards Tabula Gallus

Abstract

The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.

Fourth Report on Chicken Genes and Chromosomes 2022

“…Chicken Cell Atlas: Science and DeSci (Prepared by M. Yamagata) Chickens are not only widely consumed for their eggs and meat but are also used as a model species for biological and medical research [Stern, 2005;Burt, 2007;Haniffa et al, 2021]. To advance our understanding of this species, we need to chart the types and properties of all chicken cells across all organs and tissues, build a reference map of the mature and developing chicken bodies, and provide the resources for studying the biology of this species [Yamagata, 2022]. Similar to the mouse and human cell atlas enterprises in progress (see below), this project will generate single-cell transcriptome data for chickens, characterize each cell type, and provide foundational information integrating molecular, spatial, and temporal modalities.…”

“…Recent advances in single-cell RNA sequencing (scRNA-seq) have had significant effects on the study of complex tissues, leading to the discovery of novel cell types, cell states, and biomarkers [Stuart and Satija, 2019;Luecken and Theis, 2019;Alfieri et al, 2022;Zeng, 2022]. The scRNA-seq technology has opened up a plethora of opportunities to perform novel studies using new and classic model animals, including chickens (Gallus gallus) [Yamagata, 2022] and other birds [Chen et al, 2021;Colquitt et al, 2021]. A chicken cell atlas project (aka, DOI: 10.1159/000529376 Tabula Gallus) has been proposed to create a cell atlas of all tissues in the mature and developing chicken [Yamagata, 2022].…”

“…The scRNA-seq technology has opened up a plethora of opportunities to perform novel studies using new and classic model animals, including chickens (Gallus gallus) [Yamagata, 2022] and other birds [Chen et al, 2021;Colquitt et al, 2021]. A chicken cell atlas project (aka, DOI: 10.1159/000529376 Tabula Gallus) has been proposed to create a cell atlas of all tissues in the mature and developing chicken [Yamagata, 2022]. Like several ongoing cell atlas projects (see below), the chicken project will collect scRNA-seq data for chickens, characterize each cell type, and eventually make available information that integrates diverse modalities.…”

“…The chicken cell atlas is still in its infancy (Table 2) [Yamagata, 2022;Liu Y et al, 2022]. Nonetheless, a couple of pioneering studies have realized this endeavor, re-vealing various cell types and their states in the chick limb buds [Feregrino et al, 2019;De Lima et al, 2021], the early primitive streak stage [Vermillion et al, 2018;Guillot et al, 2021], the neural crests [Morrison et al, 2017;Gandhi et al, 2020;Williams et al, 2022], and the neural retina [Hoang et al, 2020;Tegla et al, 2020;.…”

A Primer for Single-Cell Sequencing in Non-Model Organisms

“…For example, in model organisms including humans, major initiatives are underway to develop cell atlases for tissues, organs, and the whole body through developmental stages, for example the Tabula Sapiens [ 68 ]. Similar Tabula projects for other species are also emerging [ 69 ]. The overarching goals for these atlas projects are to develop comprehensive, multiomics-based, developmental trajectories for cell lineages in complex organisms.…”