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Links from GEO DataSets

Items: 20

1.

RNAseq of regenerating yap mutant zebrafish hearts

(Submitter supplied) A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24776
12 Samples
Download data: XLSX
Series
Accession:
GSE112452
ID:
200112452
2.

siRNA knockdown of neonatal rat cardiac myocytes and fibroblasts

(Submitter supplied) Primary neonatal rat cardiac myocytes or fibroblasts were isolated and subjected to siRNA mediated Yap knockdown
Organism:
Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24782
12 Samples
Download data: XLSX
Series
Accession:
GSE112464
ID:
200112464
3.

Comparison of the expression profile of GFP-positive cells from Tg(-6.8wt1a:EGFP) with the rest of the cells in adult zebrafish cardiac ventricles

(Submitter supplied) wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP-positive cells to the rest of the cells of the ventricle.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
8 Samples
Download data: XLSX
Series
Accession:
GSE101204
ID:
200101204
4.

Comparison of the expression profiles of kdrl:mCherry-positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin-positive cells upon injury compared to the rest of cardiac cells.

(Submitter supplied) Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart, and activated endocardial kdrl:mCherry cells, postnb:citrine fibroblasts and the rest of the cells at 7 days post injury.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
16 Samples
Download data: XLSX
Series
Accession:
GSE101200
ID:
200101200
5.

postnb lineage traced cells at 7 and 60 days post cryoinjury (dpi) during adult zebrafish cardiac ventricle regeneration

(Submitter supplied) Contrary to mammals, zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast-like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP-GFP-loxP-mCherrycz1701 double transgenic line, we permanently label cells that expressed postnb at 3 and 4 days post injury (dpi) with mCherry by administration of 4-OHT. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
7 Samples
Download data: XLS
Series
Accession:
GSE101199
ID:
200101199
6.

siRNA knockdown in neonatal rat cardiac myocytes

(Submitter supplied) Primary neonatal rat cardiac myocytes were isolated and subjected to siRNA mediated Yap knockdown
Organism:
Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24782
9 Samples
Download data: XLSX
Series
Accession:
GSE121929
ID:
200121929
7.

YAP/TAZ deficiency reprograms macrophage phenotype and improves infarct healing and cardiac function after myocardial infarction

(Submitter supplied) Adverse cardiac remodeling after myocardial infarction (MI) causes structural and functional changes in the heart leading to heart failure. The initial pro-inflammatory response followed by an anti-inflammatory or reparative response post-MI is essential for minimizing the myocardial damage, healing, and scar formation. Bone marrow-derived macrophages (BMDMs) are recruited to the injured myocardium and essential for cardiac repair as they can adopt both pro-inflammatory (M1) or anti-inflammatory/reparative (M2) phenotypes to modulate inflammatory and reparative response, respectively. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
12 Samples
Download data: TXT
Series
Accession:
GSE158889
ID:
200158889
8.

Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration

(Submitter supplied) Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms, such as zebrafish, cardiac injury is followed by transient fibrosis and scar-free regeneration. The mechanisms that drive scarring versus scar-free regeneration are not well understood. Here, we show that the homeobox-containing transcription factor Prrx1b is required for scar-free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
4 Samples
Download data: CSV, TSV
Series
Accession:
GSE153170
ID:
200153170
9.

Multiple roles for Wwtr1 in cardiac wall maturation

(Submitter supplied) Cardiac trabeculation is a highly regulated process that starts with the delamination of cardiomyocytes from the compact wall to form stereotypical muscular ridges in the developing ventricle.  The Hippo signaling pathway has been implicated in cardiac development but many questions remain.  We investigated the role of Wwtr1, a nuclear effector of the Hippo pathway, in zebrafish and find that its loss results in hearts with reduced trabeculation. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
6 Samples
Download data: TXT
Series
Accession:
GSE103169
ID:
200103169
10.

Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13692 GPL16331
16 Samples
Download data: BED, BEDGRAPH, GPR
Series
Accession:
GSE138062
ID:
200138062
11.

Cardiac profiling of Yap-bound chromatin in neonatal Salvador mutant mice

(Submitter supplied) In this study, we identified chromatin regions bound by YAP, a major effector of the Hippo tumor suppressor pathway. To disrupt Hippo signaling in the mouse heart, we inactivated the single mammalian Salv ortholog using a Salv conditional null allele and and tamoxifen inducible Myh6-cre/Esr1 allele, Cre activity was induced with 4 consecutive intraperitoneal (i.p.) or subcutaneous injections of tamoxifen from P7-P10.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL16331
4 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE46529
ID:
200046529
12.

Cardiac gene expression profiling of neonatal Salvador mutant mice

(Submitter supplied) In this study, we identified a number of genes whose expression are regulated by the Hippo tumor suppressor pathway. To disrupt Hippo signaling in the mouse heart, we inactivated the single mammalian Salv ortholog using a Salv conditional null allele and the Nkx2.5 cre allele that directs cardiac cre activity. Total RNA from P8-stage hearts were used for expression profiling.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL13692
12 Samples
Download data: GPR
Series
Accession:
GSE44103
ID:
200044103
13.

Gene expression analysis of wt1b-positive cardiac macrophages

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL14664 GPL18413
16 Samples
Download data: TXT
Series
Accession:
GSE118509
ID:
200118509
14.

Comparison of the gene expression expression profile of activated and resting epicardium

(Submitter supplied) Zebrafish can regenerate their hearts. As a first response to injury, the epicardium reacts by upregulalion of developmental marker genes. Here we compared in an unbiased manner the expression of the epicardium from uninjured zebrafish hearts and hearts at 3 days postcryoinjury. To label epicardial cells of uninjured hearts we usd pard3:GFP (POon et al 2010) and to label epicardium of the injured heart wt1b:eGFP (Perner et al 2007)
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL14664
8 Samples
Download data: TXT, XLS
Series
Accession:
GSE118457
ID:
200118457
15.

Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart

(Submitter supplied) Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
8 Samples
Download data: XLS
Series
Accession:
GSE115381
ID:
200115381
16.

ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration

(Submitter supplied) RNA-seq comparing WT and caERBB2 over expresising hearts with/out injury
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
16 Samples
Download data: XLSX
Series
Accession:
GSE144391
ID:
200144391
17.

Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

(Submitter supplied) The adult mammalian heart heals after myocardial infarction (MI) by deposition of scar tissue, leading to downstream arrhythmia, remodelling and heart failure1. In contrast, adult zebrafish and neonatal mouse hearts are capable of regenerating after injury. Macrophages are key mediators of tissue repair and appear to be required for both regeneration and healing by scar formation, but the mechanisms underlying these distinct roles are poorly understood2-4. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
28 Samples
Download data: XLS
Series
Accession:
GSE126772
ID:
200126772
18.

Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

(Submitter supplied) Canonical roles for macrophages in mediating the fibrotic response after a heart attack (myocardial infarction) include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition. Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
21 Samples
Download data: BW, TXT
Series
Accession:
GSE100029
ID:
200100029
19.

Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish 

(Submitter supplied) During heart regeneration in the zebrafish, fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre-existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here, using sox10 genetic fate mapping, we identified a subset of pre-existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively after cryoinjury. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23274
25 Samples
Download data: TXT
Series
Accession:
GSE133571
ID:
200133571
20.

­runx1 controls zebrafish heart regeneration by promoting scar deposition as well as inhibiting myocardial proliferation and survival

(Submitter supplied) Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types, during both development and adulthood. Here, we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration, but unexpectedly, absence of runx1 results in enhanced regeneration. Using single cell sequencing, we found that the wild-type injury site consists of Runx1-positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without differentiating into myofibroblasts. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
3 Samples
Download data: H5
Series
Accession:
GSE138181
ID:
200138181
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