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Series GSE74652 Query DataSets for GSE74652
Status Public on Jan 11, 2016
Title Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary In contrast to mammals, zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here, we show that tomo-seq can be used to identify whole-genome transcriptional profiles of the injury zone, the border zone and the healthy myocardium. Interestingly, the border zone is characterized by the re-expression of embryonic cardiac genes that are also activated after myocardial infarction in mouse and human, including targets of Bone Morphogenetic Protein (BMP) signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast, we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation, ultimately compromising myocardial regeneration, while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non-regenerative hearts.
 
Overall design To generate spatially-resolved RNA-seq data for injured zebrafish hearts (3 and 7 days-post-injury), we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing.
 
Contributor(s) Kruse FK, Wu C, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noël ES, Grün D, Eugene B, Engel FB, van Oudenaarden A, Weidinger G, Bakkers J
Citation(s) 26748692
Submission date Nov 03, 2015
Last update date May 15, 2019
Contact name Fabian Klaus Kruse
E-mail(s) f.kruse@hubrecht.eu
Organization name Hubrecht Institute
Lab Jeroen Bakkers
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platforms (1)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (2)
GSM1924887 zebrafish-heart_WT_3dpi_#1
GSM1924888 zebrafish-heart_WT_7dpi_#1
Relations
BioProject PRJNA302179
SRA SRP066192

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE74652_RAW.tar 590.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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