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| Status |
Public on Apr 14, 2022 |
| Title |
Mapping the cardiac vascular niche in heart failure |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Various transgenic CreER;tdTomato mouse-lines (Pdgfrb-CreER, Col1a1-CreER, Gli1-CreER, Cdh5-CreER, Myh11-CreER, Ng2-CreER) were pulsed with tamoxifen and subjected to either Sham or TAC surgery at 21 days after tamoxifen induction. Two and four weeks later, tdTomato-positive cells were isolated from hearts by FACS sorting and 10x Genomics scRNA 3'RNA sequencing pipeline was applied. We identified fibroblast, endothelial cells, mural cells and Schwann cells as major cardiac cell types in our samples. Gene expression changes between subtypes of the major cell types point towards a general upregulation of extra cellular matrix related genes, with fibroblasts being the highest producer.
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| Overall design |
We used scRNA 3' RNA sequencing product from 10x Genomics to trace vascular and perivascular cell types of the heart in murine pressure overload induced heart failure.
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| Contributor(s) |
Peisker F, Halder M, Nagai J, Li R, Möllmann J, Lehrke M, Schneider RK, Costa I, Kramann R |
| Citation(s) |
35641541 |
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| Submission date |
Feb 08, 2021 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Fabian Peisker |
| Organization name |
Uniklinikum RWTH Aachen
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| Street address |
Pauwelsstraße 30
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| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA700769 |
| SRA |
SRP305417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE166403_RAW.tar |
7.5 Gb |
(http)(custom) |
TAR (of H5, HTML) |
| GSE166403_tdTomato.fa.gz |
643 b |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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