Spatially resolved RNA-sequencing of the injured murine heart
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA433421 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Myocardial infarction results in a massive loss of cardiomyocytes which will not be regenerated. Recent studies using models of regeneration show that cardiomyocytes at the border of the injury are most prone to proliferate. Which processes occur in this region and make these cells act as progenitors, remains to be elucidated. In addition, we lack molecular markers for the identification of these cells in the human heart. To create a transcriptional profile of the murine border zone, identifying local processes and enabling the discovery of marker genes which will allow the identification of human cardiomyocytes with potential proliferative capacity. Myocardial infarction (MI) was induced in mice and 3, 7 or 14 days later ventricular tissue was isolated ranging from the injured area into the remote myocardium. Tomo-sequencing was performed on these cardiac tissue samples, which comprises of tissue sectioning together with RNA-sequencing on individual sections. This resulted in spatially resolved transcriptome maps containing a dynamic, transcriptionally distinct border zone with reduced expression of genes involved in mitochondrial oxidative phosphorylation, fatty acid metabolism and sarcomere function and increased expression of myofibroblast and proliferation genes. Genes shared between the murine and zebrafish border zone, such as ANKRD1, UCHL1 and DES, were validated as molecular markers in injured human hearts. Unexpectedly, pronounced expression of these marker genes was found in surviving cardiomyocytes located at the sub-endocardium. The border zone is an evolutionary conserved, transcriptionally distinct and dynamic region. With the use of newly identified markers, we discovered the existence of sub-endocardial cardiomyocytes in ischemic human hearts that share transcriptional characteristics with potential progenitor cells. This might have far reaching implications for the development of strategies to stimulate the regenerative capacity of patients suffering from ischemic injury.
2025-02-07 | GSE110314 | GEO
Project description:Spatially resolved RNA-sequencing of the embryonic zebrafish heart
| PRJNA408129 | ENA
Project description:Development of specialized cell types and structures in the vertebrate heart is regulated by spatially-restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo-seq, combining high-throughput RNA sequencing with tissue sectioning, to establish a genome-wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub-compartments. Pacemaker cells in the sinoatrial region induce heart contractions, but little is known about the mechanisms underlying their development and function. Using our transcriptome map, we identified spatially restricted Wnt/β-catenin signaling activity in pacemaker cells, which was controlled by Islet-1 activity. Moreover, Wnt/β-catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus, this high-resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially-restricted molecular pathways critical for specific cardiac functions.
2018-02-06 | GSE104057 | GEO
Project description:The recent development of spatial omics enables single-cell profiling of the transcriptome and the 3D organization of the genome in a spatially resolved manner. A spatial epigenomics method would expand the repertoire of spatial omics tools and accelerate our understanding of the spatial regulation of cellular processes and tissue functions. Here, we developed an imaging approach for spatially resolved profiling of epigenetic modifications in single cells
2022-12-16 | GSE191069 | GEO
Project description:Using an experimental TBI rat model of mild/moderate Controlled Cortical Impact (CCI) injury, we combined large-scale proteomics identification and relative quantification using Spatially-Resolved Microproteomics with MALDI MS Imaging of Lipids. Spatially by studying different regions in the brain post injury in a coronal view, with main focus on the injury site itself. Temporally by studying the acute and subacute phase post injury, including injured rat brains at 1 day, 3 days, 7 days, and 10 days post injury. Direct on-tissue micro-digestion followed by micoextraction from 1 mm2 surface area within the injured cortical tissue were subjected to LC-MS & MS/MS analysis using HR MS. In addition, several identified potential biomarkers within our study were used to stimulate dorsal root ganglion (DRG), astrocyte, and macrophage cell lines to obtain a better understanding of their role and contribution in the injury.
2019-06-19 | PXD011262 | Pride
Project description:Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model
| PRJNA758384 | ENA
Project description:Understanding the spatial distribution of T cells is pivotal to decrypting immune dysfunction in cancer. Current spatially resolved transcriptomics fall short in directly annotating T cell receptors (TCRs), limiting the comprehension of anti-cancer immunity. We introduce a novel technology, Spatially Resolved T Cell Receptor Sequencing (SPTCR-seq), integrating target enrichment and long-read sequencing for highly sensitive TCR sequencing. This approach yields an on-target rate of ~85%, and via a bespoke computational pipeline, it provides meticulous spatial mapping, error correction, and UMI refinement. SPTCR-seq outperforms PCR-based methods, offering superior reconstruction of the complete TCR architecture, inclusive of V, D, J regions and the vital complementarity-determining region 3 (CDR3). Applying SPTCR-seq, we reveal local T cell diversity, clonal expansion, and transcriptional evolution across spatially distinct niches in glioblastoma, identifying critical involvement of NK and B cells in spatial T cell adaptation. SPTCR-seq, by bridging spatially resolved omics and TCR sequencing, stands as a robust tool for exploring T cell dysfunction in cancers and beyond.
2023-07-25 | GSE238071 | GEO
Project description:A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution
| PRJNA941825 | ENA
Project description:Spatially resolved multiomics of human cardiac niches - Visium
| PRJEB62497 | ENA
Project description:Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and limited treatment options. Efforts to identify effective treatments are thwarted by limited understanding of IPF pathogenesis and poor translatability of available preclinical models. To address these limitations, we generated spatially resolved transcriptome maps of human IPF and bleomycin-induced mouse lung fibrosis.
2024-05-21 | GSE267904 | GEO