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Series GSE122403 Query DataSets for GSE122403
Status Public on May 30, 2019
Title Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The heart is a complex organ composed of multiple cell and tissue types. During early developmental stages, heart cells from different regions of the heart exhibit different patterns of gene expression, which are thought to significantly contribute to heart development and morphogenesis. Until recently, the lack of adequate tools prevented our ability to systematically profile gene expression in a cell type and anatomically-specific manner during heart development. Single cell RNA sequencing has emerged as a powerful approach that allows genome-wide analysis of gene expression in single cells. Using microfluidic-chip and droplet-based single-cell RNA sequencing platforms, we analyze cardiac cells during the early stages of heart development. We found, by principle component analysis, that the expression of cell cycle genes represents a major determinant of transcriptional variation in all analyzed cardiac cell types. Interestingly, when single cardiomyocytes (CMs) from different heart chambers were analyzed, we found that atrial ventricular canal derived CMs have reduced cell cycle activity compare with CMs from the left and right ventricular chambers. In addition, CMs in the trabecular myocardium exhibit reduced cell cycle activity than CMs in the compact myocardium. When CMs within the same chamber were segregated by their cell cycle phase, we found that CMs in the G2/M phase downregulate their sarcomeric and cytoskeletal markers. Finally, we revealed the expression of a signaling ligand from the endocardium that may repress trabecular CM proliferation, and an epicardial-derived ligand that can promote compact CM proliferation. Together these data highlight the variations in cell cycle activity to selectively promote cardiac chamber growth during development and the profound transcriptional shift within the same cell at different phases of cell cycle. Identifying alterations in the expression of key signaling molecules that drive CM proliferation may lead to greater understanding of the onset or progression of congenital heart disease.
Overall design Single cell transcriptional analysis of embryonic cardiac cells using 10x Genomics 3' solution.
Contributor(s) Li G, Wu S
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Submission date Nov 09, 2018
Last update date Jun 01, 2019
Contact name Guang Li
Organization name University of Pittsburgh
Department Developmental Biology
Lab Guang Li lab
Street address 530 45th St. 8116 Rangos Research Center
City Pittsburgh
State/province PA
ZIP/Postal code 15201
Country USA
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (1)
GSM3465996 e10.5_heart_ventriculars
BioProject PRJNA504900
SRA SRP168392

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Supplementary file Size Download File type/resource
GSE122403_RAW.tar 87.4 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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