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A 3D molecular atlas of the chick embryonic heart

Anderson, Claire, Hill, Bill, Lu, Hui-Chun, Moverley, Adam, Yang, Youwen, Oliveira, Nidia M.M., Baldock, Richard A., Stern, Claudio D.
Developmental biology 2019
chicks, developmental stages, gene expression, genes, heart, in situ hybridization, mice, sequence analysis, tomography
We present a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 micro-dissected regions reveals regionalised expression of 15,570 genes. Of these, 132 were studied by in situ hybridisation and a subset (38 genes) was mapped by Optical Projection Tomography or serial sectioning to build a detailed 3-dimensional atlas of expression. We display this with a novel interactive 3-D viewer and as stacks of sections, revealing the boundaries of expression domains and regions of overlap. Analysis of the expression domains also defines some sub-regions distinct from those normally recognised by anatomical criteria at this stage of development, such as a previously undescribed subdivision of the atria into two orthogonal sets of domains (dorsoventral and left-right). We also include a detailed comparison of expression in the chick with the mouse and other species.