Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA385529 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5511310.fastq.gz | Fastqsanger.gz | |||
| SRR5511320.fastq.gz | Fastqsanger.gz | |||
| SRR5511330.fastq.gz | Fastqsanger.gz | |||
| SRR5511340.fastq.gz | Fastqsanger.gz | |||
| SRR5511350.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 574 |
Similar Datasets
Project description:High throughput single-cell whole transcriptome analysis of induced cardiomyocytes during direct cardiac reprogramming [Bulk-seq]
| PRJNA385605 | ENA
Project description:Analysis of induced cardiomyocytes during direct cardiac reprogramming
| PRJNA385601 | ENA
Project description:Whole transcriptome analysis of induced cardiomyocytes during direct cardiac reprogramming [expression]
| PRJNA385604 | ENA
Project description:Direct conversion of cardiac fibroblast into functional induced cardiomyocytes by forced expression of three cardiac transcription factors, Mef2c, Gata4, and Tbx5, holds great promise for regenerative medicine. Cardiac reprogramming consists of waves of transcription remodeling events, including the fast acquisition of cardiac program and the gradual loss of fibroblast program. However, how this transcription remodeling was driven by the upstream chromatin landscape is still unclear. In this study, we performed single-cell ATAC-seq on Day 3 cardiac reprogramming cells and unveiled networks of transcription factors (TFs) playing a pivotal role in the shift of chromatin accessibility during the early stage of cardiac reprogramming. Moreover, integration analysis of scRNA-seq and scATAC-seq lead to the identification of active TFs function as barriers to cardiac reprogramming.
2021-09-05 | GSE171525 | GEO
Project description:The reprogramming of fibroblast cells to induced pluripotent stem (iPS) cells raises the possibility that a somatic cell could be reprogrammed to an alternative differentiated fate without first becoming a stem/progenitor cell. A large pool of fibroblast cells exists in the post-natal heart, yet no single “master regulator” of direct cardiac reprogramming has been identified. Here, we report that a combination of three developmental transcription factors (i.e., Gata4, Mef2c and Tbx5) rapidly and efficiently reprogrammed post-natal cardiac or tail-tip fibroblasts directly into differentiated cardiomyocyte-like cells. Induced cardiomyocytes expressed cardiac-specific markers, had a global gene expression profile similar to cardiomyocytes, and contracted spontaneously. Fibroblast cells transplanted into mouse hearts one day after transduction of the three factors also differentiated into cardiomyocyte-like cells. These findings demonstrate that functional cardiomyocytes can be directly reprogrammed from differentiated somatic cells by defined factors. Reprogramming of endogenous or explanted fibroblast cells might provide a source of cardiomyocytes for regenerative approaches.
2010-06-12 | GSE22292 | GEO
Project description:Adult cardioyocytes undergo remarkable dedifferentiation and cell cycle reprogramming/reentery when cultured in mitogen-rich medium, continuously, and give rise to cardiac progenitor cells (CPCs). Using microfluidic device for single-cell capture and whole-transcriptomic amplification, we analyze the whole-genome transcriptomic profile in adult mouse cardiomyocytes (Ctl) and in their derived CPCs, and validate the gene expression by single-cell PCR and PCR array. Using two platforms for DNA methylation profiling: NimbleGen DNA methylation array and CHARM array, the whole-genome DNA methylation profile in myocytes (Ctl) and CPCs were compared and their regulations in relationship to the transcriptomics profile were analyzed. The results demonstrated remarkable molecular reprogramming pertaining to dedifferentiation, loss of cardiac contractile, structure, and function molecules, and reactivation of cell cycle and proliferation genes, significant changes in metabolisms. The reduction of cardiac function and structure genes are highly related to their hypermethylation of the promoter regions. GO and Pathway enrichment analysis revealed distinct coordianted transcriptomic and epigenetic regulation in the CPCs derived from cardiomyocytes. Mouse single cardiomyocytes (Ctl) and their derievd single CPCs were captured using microfluidic deviced and cDNA synthesized and amplified and labelled using NuGENE kits, and regular Affymetrix hybridization and wash protocols were used to process the mouse whole-genome array GeneChip 430 2.0.
2016-07-24 | E-GEOD-49448 | biostudies-arrayexpress
Project description:Direct cardiac reprogramming converts fibroblasts into induced cardiomyocytes (iCMs) with the minimal combination of transcription factors, Gata4 (G), Mef2c (M), and Tbx5 (T). However, the induction of functional mature iCMs is inefficient and the mechanisms remain elusive. Mef2c is a central transcription factor in direct cardiac reprogramming. We investigated the effect of Mef2c isoforms(M1, M2, M6) and transcriptional activity (M2TAD) on cardiac reprogramming on cardiac reprogramming. Then, we found that the active form of Mef2c evoked epigenetic remodeling cooperating with p300 and promoted the maturation of iCMs.
2023-06-13 | GSE196293 | GEO
Project description:Direct lineage conversion holds great promise in the regenerative medicine field for restoring damaged tissues using functionally engineered counterparts. However, current methods of direct lineage conversion, even those employing virus-mediated transgenic expression of tumorigenic factors, are extremely inefficient (~25%). Thus, advanced methodologies capable of revolutionizing efficiency and addressing safety issues are key to clinical translation of these technologies. Here, we propose an exosome-guided, non-viral, direct-lineage conversion strategy to enhance transdifferentiation of fibroblasts to induced cardiomyocyte-like cells (iCMs). Exosomes produced during the cardiac differentiation process of embryonic stem cells (ESCs) are able to achieve extremely high reprogramming efficiency (>60%) by generating functional iCMs from mouse embryonic fibroblasts via a cardiac precursor-like stage rather than a pluripotent state. The resulting iCMs possess typical cardiac Ca2+ transients and electrophysiological features, and exhibit global gene expression profiles similar to those of cardiomyocytes. The optimized reprogramming conditions produce beating iCM clusters ~3-fold more efficiently than conventional methods. This is the first demonstration of the use of exosomes derived from ESCs undergoing cardiac differentiation as biomimetic tools to induce direct cardiac reprogramming with greatly improved efficiency, establishing a general, more readily accessible platform for broadly generating a variety of specialized somatic cells through direct lineage conversion.
2022-03-02 | GSE166249 | GEO
Project description:Direct lineage conversion holds great promise in the regenerative medicine field for restoring damaged tissues using functionally engineered counterparts. However, current methods of direct lineage conversion, even those employing virus-mediated transgenic expression of tumorigenic factors, are extremely inefficient (~25%). Thus, advanced methodologies capable of revolutionizing efficiency and addressing safety issues are key to clinical translation of these technologies. Here, we propose an exosome-guided, non-viral, direct-lineage conversion strategy to enhance transdifferentiation of fibroblasts to induced cardiomyocyte-like cells (iCMs). Exosomes produced during the cardiac differentiation process of embryonic stem cells (ESCs) are able to achieve extremely high reprogramming efficiency (>60%) by generating functional iCMs from mouse embryonic fibroblasts via a cardiac precursor-like stage rather than a pluripotent state. The resulting iCMs possess typical cardiac Ca2+ transients and electrophysiological features, and exhibit global gene expression profiles similar to those of cardiomyocytes. The optimized reprogramming conditions produce beating iCM clusters ~3-fold more efficiently than conventional methods. This is the first demonstration of the use of exosomes derived from ESCs undergoing cardiac differentiation as biomimetic tools to induce direct cardiac reprogramming with greatly improved efficiency, establishing a general, more readily accessible platform for broadly generating a variety of specialized somatic cells through direct lineage conversion.
2022-03-02 | GSE166250 | GEO
Project description:Adult cardioyocytes undergo remarkable dedifferentiation and cell cycle reprogramming/reentery when cultured in mitogen-rich medium, continuously, and give rise to cardiac progenitor cells (CPCs). Using microfluidic device for single-cell capture and whole-transcriptomic amplification, we analyze the whole-genome transcriptomic profile in adult mouse cardiomyocytes (Ctl) and in their derived CPCs, and validate the gene expression by single-cell PCR and PCR array. Using two platforms for DNA methylation profiling: NimbleGen DNA methylation array and CHARM array, the whole-genome DNA methylation profile in myocytes (Ctl) and CPCs were compared and their regulations in relationship to the transcriptomics profile were analyzed. The results demonstrated remarkable molecular reprogramming pertaining to dedifferentiation, loss of cardiac contractile, structure, and fucntion molecules, and reactivation of cell cycle and proliferation genes, significant changes in metabolisms. The reduction of cardiac function and structure genes are highly related to their hypermethylation of the promoter regions. GO and Pathway enrichment analysis revealed distinct coordianted transcriptomic and epigenetic regulation in the CPCs derived from cardiomyocytes. Genomic DNA isolated from adult mouse cardiomyocytes (Ctl) or cardiomyocyte-derived progenitor cells (CPCs) was subjected to digestion by methylcytosine-sensitive enzyme McrBC, and subsequently purification and amplification, labeling and hybridization to the NimbleGen 3x720K DNA methylation Promoter array, according to NimbleGen protocol. Percentage methylation, hypermethylation or hypomethylation, and peak enrichment were assessed using CHARM protocol.
2016-07-24 | E-GEOD-49678 | biostudies-arrayexpress