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Links from GEO DataSets

Items: 20

1.

H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA-seq]

(Submitter supplied) We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration. Specifically, we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
6 Samples
Download data: CSV, TDF
Series
Accession:
GSE96929
ID:
200096929
2.

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration

(Submitter supplied) Deciphering the genetic and epigenetic regulation of cardiomyocyte proliferation in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic changes in gene expression concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20828 GPL14875
19 Samples
Download data: TDF
Series
Accession:
GSE96930
ID:
200096930
3.

H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [ChIP-seq]

(Submitter supplied) Deciphering the genetic and epigenetic regulation of injury-induced heart regeneration in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic gene expression changes concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20828
13 Samples
Download data: CSV, TDF
Series
Accession:
GSE96928
ID:
200096928
4.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL21741
16 Samples
Download data: BED
Series
Accession:
GSE81893
ID:
200081893
5.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [RNA]

(Submitter supplied) We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding transcriptional changes during adult models of regeneration.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
4 Samples
Download data: TXT
Series
Accession:
GSE81865
ID:
200081865
6.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H3K27Ac]

(Submitter supplied) We report high-throughput profiling of acetylation of lysine 27 on histone H3 from whole zebrafish ventricles. The H3K27Ac mark has been shown to be present at active enhancer elements and including regions of active chromatin. We profile H3K27Ac in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21741
2 Samples
Download data: BED
Series
Accession:
GSE81863
ID:
200081863
7.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H33]

(Submitter supplied) We report high-throughput profiling of transgenic histone H3.3 in zebrafish cardiomyocytes. The replacement histone H3.3 is deposited at sites of nucleosome turnover including regions of active chromatin. We profile H3.3 in uninjured cardiomyocytes, those undergoing regeneration 14 days after genetic ablation and those proliferating 7 days after Nrg1 stimulated hyperplasia. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21741
10 Samples
Download data: BED
Series
Accession:
GSE81862
ID:
200081862
8.

AP-1 Regulates Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion during Zebrafish Heart Regeneration

(Submitter supplied) The zebrafish has emerged as a powerful model to study cardiac regeneration; however, the mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Here, we show that AP-1 transcription factors play an essential role in regulating the cardiomyocyte response. Using ATAC-Seq, we first find that the cardiomyocyte chromatin accessibility landscape is dynamic following cryoinjury, and that AP-1 motifs are the most highly enriched in regions that gain accessibility during regeneration. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20828
14 Samples
Download data: TXT
Series
Accession:
GSE130940
ID:
200130940
9.

RNA sequencing analyses of grl/hey2-overexpressing hearts and control hearts, as well as grl/hey2-deficient hearts and wild-type hearts following ventricular resection at 7 dpa

(Submitter supplied) As Grl/Hey2 directly binds DNA through E box motifs and mediates transcription repression, we aim to gain insights into potential target genes of Grl/Hey2 during heart regeneration. We performed RNA-seq analyses using total RNAs collected from 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts and Tg(cmlc2:nRSGG) control hearts, as well as grl5nt-/- mutant hearts and wild-type hearts following ventricular resection at 7 dpa. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23085
12 Samples
Download data: XLS, XLSX
Series
Accession:
GSE129499
ID:
200129499
10.

Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.

(Submitter supplied) 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. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
2 Samples
Download data: CSV
Series
Accession:
GSE74652
ID:
200074652
11.

Transcription profiling of zebrafish fin regeneration

(Submitter supplied) We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9319
4 Samples
Download data: TXT
Series
Accession:
GSE76564
ID:
200076564
12.

Modulation of tissue repair by regeneration enhancer elements.

(Submitter supplied) We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL14875 GPL9319
8 Samples
Download data: TXT, WIG
Series
Accession:
GSE75894
ID:
200075894
13.

Single-cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.

(Submitter supplied) While the heart regenerates poorly in mammals, efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration, resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However, there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
4 Samples
Download data: CSV, TSV
Series
Accession:
GSE139218
ID:
200139218
14.

Leveraging chromatin state transitions for regulatory networks identification in heart regeneration

(Submitter supplied) The limited regenerative capacity of the human heart is responsible for the high morbidity and mortality world-wide. In contrast, zebrafish possess a robust regenerative capacity. Here, we have characterized the chromatin state transitions during zebrafish heart regeneration and interrogated how gene expression patterns are orchestrated. We found a massive gain of repressive chromatin marks one day after myocardial injury, followed by a large-scale acquisition of active chromatin characteristics on day 4 and a switch to a repressive state on day 14. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21930
50 Samples
Download data: BW
Series
Accession:
GSE211677
ID:
200211677
15.

RNA-seq experiments on heart regeneration in WT, foxm1 and dusp6 mutants.

(Submitter supplied) The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 days post amputation (dpa). Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment, bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
12 Samples
Download data: XLSX
Series
Accession:
GSE201139
ID:
200201139
16.

Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL17021
18 Samples
Download data
Series
Accession:
GSE95764
ID:
200095764
17.

Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration [ATAC-Seq]

(Submitter supplied) Background - The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we construct a transcriptional atlas of multiple cardiac cell populations, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: TXT
Series
Accession:
GSE95763
ID:
200095763
18.

Multi-cellular Transcriptional Profiling Reveals an Epigenetic Barrier to Adult Heart Regeneration [RNA-Seq]

(Submitter supplied) Background - The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we construct a transcriptional atlas of multiple cardiac cell populations, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
9 Samples
Download data: TXT
Series
Accession:
GSE95762
ID:
200095762
19.

Multicellular Transcriptional Analysis of Mammalian Heart Regeneration

(Submitter supplied) The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we construct a transcriptional atlas of multiple cardiac cell populations, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
64 Samples
Download data: TXT, XLSX
Series
Accession:
GSE95755
ID:
200095755
20.

In vivo activation of a conserved microRNA program induces robust mammalian heart regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Rattus norvegicus; synthetic construct
Type:
Non-coding RNA profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL14613 GPL18694
7 Samples
Download data: CEL
Series
Accession:
GSE62389
ID:
200062389
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