@article{222fe76139ab47dc87b4ba4333de83cc,
title = "3D-cardiomics: A spatial transcriptional atlas of the mammalian heart",
abstract = "Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from http://3d-cardiomics.erc.monash.edu/.",
keywords = "3D organ, Bioinformatics, Cardiac model, Cardiac systems, Data visualization, Spatial transcriptomics, Systems biology",
author = "Monika Mohenska and Tan, {Nathalia M.} and Alex Tokolyi and Furtado, {Milena B.} and Costa, {Mauro W.} and Perry, {Andrew J.} and Jessica Hatwell-Humble and {van Duijvenboden}, Karel and Nim, {Hieu T.} and Ji, {Yuan M. M.} and Natalie Charitakis and Denis Bienroth and Francesca Bolk and Celine Vivien and Knaupp, {Anja S.} and Powell, {David R.} and Elliott, {David A.} and Porrello, {Enzo R.} and Nilsson, {Susan K.} and {del Monte-Nieto}, Gonzalo and Rosenthal, {Nadia A.} and Rossello, {Fernando J.} and Polo, {Jose M.} and Mirana Ramialison",
note = "Funding Information: J.M.P. was funded by a Sylvia-Charles Viertel Fellowship and an ARC Future Fellowship. M.R. was funded by the Sun Foundation, an NHMRC/Heart Foundation Career Development Fellowship (1049980), ARC Discovery Project Grant (DP190102771) and an NHMRC Ideas Grant (APP1180905). A.T. was supported by a Biomedical Research Victoria UROP/CSL scholarship. G.dM.N. was funded by a Heart Foundation Future Leader Fellowship (102036) and ARC Discovery Project Grant (DP190101475). E.R.P. and D.A.E. acknowledge grant and fellowship support from The Stafford Fox Medical Research Foundation and the Royal Children's Hospital Foundation . MCRI is supported by the Victorian Government's Operational Infrastructure Support Program . The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. Publisher Copyright: {\textcopyright} 2021",
year = "2022",
month = feb,
day = "1",
doi = "https://doi.org/10.1016/j.yjmcc.2021.09.011",
language = "English",
volume = "163",
pages = "20--32",
journal = "Journal of molecular and cellular cardiology",
issn = "0022-2828",
publisher = "Academic Press Inc.",
}