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Items: 1 to 20 of 34639

1.

Analysis of gene expression in zebrafish cornea during wound healing

(Submitter supplied) The cornea, transparent and outermost structure of camera-type eyes, is prone to environmental challenges, but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study, we report rapid wound closure after zebrafish corneal epithelium abrasion. Furthermore, by investigating the cellular and molecular events taking place during corneal epithelial closure, we show the induction of a bilateral response to a unilateral wound. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
8 Samples
Download data: XLSX
Series
Accession:
GSE193784
ID:
200193784
2.

Transcriptome analysis of young and old zebrafish ventricles

(Submitter supplied) The gradual decline of tissue functionality is the main reason why humans suffer from age-related diseases. The prevalence for cardiovascular diseases increases with increasing age. In order to prevent age-related cardiac diseases, it is of importance to understand the respective age-associated risk factors. We have therefore compared the ventricular transcriptome of old and young hearts of the model organism zebrafish. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
6 Samples
Download data
Series
Accession:
GSE182979
ID:
200182979
3.

Activation of innate immune pathways after brain injury promotes scar formation and impairs tissue recovery

(Submitter supplied) Scar formation is a major hindrance to central nervous system regeneration upon traumatic injury. Glial cells are key players during the wound healing process, and their reaction to injury determines the extent of tissue restoration. Here, we used the regenerative potential of the zebrafish telencephalon to identify specific molecular and cellular mechanisms regulating glial scar formation. We demonstrated that contact of the cerebrospinal fluid with the brain parenchyma after injury activates toll-like receptor 2 (Tlr2) and the chemokine receptor 3 (Cxcr3) innate immunity pathways leading to initiation of a glial scar. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL16933
30 Samples
Download data: CEL
Series
Accession:
GSE98217
ID:
200098217
4.

scRNA-seq of fin and body zebrafish melanocytes

(Submitter supplied) Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet, or under the nails3. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
4 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE181748
ID:
200181748
5.

Bulk RNA-seq of fin and body melanocytes and microenvironments

(Submitter supplied) Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: (1) cell lineage: melanocyte vs bulk microenvironment, (2) anatomic location: fin vs body, (3) genotype: wildtype vs CRKL,GAB2,TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
24 Samples
Download data: CSV, TAB
Series
Accession:
GSE158538
ID:
200158538
6.

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA-seq2]

(Submitter supplied) Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
5 Samples
Download data: TXT
Series
Accession:
GSE169689
ID:
200169689
7.

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL25922 GPL18413
26 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE158101
ID:
200158101
8.

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development

(Submitter supplied) We used single cell-RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1-mutant cd41-GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic (2.5 days post fertilization, dpf) and larval stages (6, 10 16 dpf).
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25922
9 Samples
Download data: MTX, TSV
Series
Accession:
GSE158099
ID:
200158099
9.

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development

(Submitter supplied) Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
6 Samples
Download data: TXT
Series
Accession:
GSE158098
ID:
200158098
10.

mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without gut microbiota.

(Submitter supplied) In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota, comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
8 Samples
Download data: TXT
Series
Accession:
GSE150376
ID:
200150376
11.

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Mus musculus; Gallus gallus; Sus scrofa; Mesocricetus auratus; Macaca mulatta; Homo sapiens
Type:
Expression profiling by high throughput sequencing
8 related Platforms
147 Samples
Download data: CSV, H5, JSON, PNG, TXT
Series
Accession:
GSE192742
ID:
200192742
12.

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (single cells)

(Submitter supplied) Analysis of CITE-seq data , Nuclei RNA-seq data and single cell RNA-seq data on CD45+ and CD45- cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar), from healthy and steatotic human livers, from hamster liver, pig liver, chicken liver, monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers, NAFLD mouse livers, healthy human livers and steatotic human livers.
Organism:
Sus scrofa; Mus musculus; Danio rerio; Gallus gallus; Macaca mulatta; Mesocricetus auratus
Type:
Expression profiling by high throughput sequencing
7 related Platforms
132 Samples
Download data: H5, TSV, TXT
Series
Accession:
GSE192740
ID:
200192740
13.

Amino acid primed mTOR activity is essential for heart regeneration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
11 Samples
Download data
Series
Accession:
GSE188244
ID:
200188244
14.

Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA-seq]

(Submitter supplied) Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously, mouse neonates and zebrafish, larvae or adult, are able to regenerate their hearts via cardiomyocyte de-differentiation and proliferation. However, a molecular mechanism of why these cardiomyocytes can re-enter cell cycle is poorly understood. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
8 Samples
Download data: TXT
Series
Accession:
GSE188243
ID:
200188243
15.

Amino acid primed mTOR activity is essential for heart regeneration [scRNA-seq]

(Submitter supplied) Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously, mouse neonates and zebrafish, larvae or adult, are able to regenerate their hearts via cardiomyocyte de-differentiation and proliferation. However, a molecular mechanism of why these cardiomyocytes can re-enter cell cycle is poorly understood. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
3 Samples
Download data: TXT
Series
Accession:
GSE184914
ID:
200184914
16.

Tfap2b specifies an embryonic melanocyte stem cell population that retains adult multi-fate potential

(Submitter supplied) Melanocytes, our pigment producing cells, originate from neural crest-derived progenitors during embryogenesis and from multiple stem cell niches in adult tissues. Although pigmentation traits are known risk-factors for melanoma, we lack lineage markers with which to identify melanocyte stem cell populations and study their function. Here, by combining live-imaging, scRNA-seq and chemical-genetics in zebrafish, we identify the transcription factor Tfap2b as a functional marker for the melanocyte stem cell (MSC) population that resides at the dorsal root ganglia site. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
2 Samples
Download data: CSV
Series
Accession:
GSE178364
ID:
200178364
17.

Regulation of chromatin accessibility in early zebrafish embryos by Pou5f3 and Sox19b transcription factors.

(Submitter supplied) Pou5f3 and Sox19b transcription factors promote chromatin accessibility and activate zygotic transcription in zebrafish embryos. It is poorly understood how two transcription factors act together on chromatin. To answer this question, we performed Omni-ATAC-seq on the zebrafish embryos, single and double mutants by Pou5f3 and Sox19b, as well as the wild-type, at two blastula developmental stages, oblong and dome. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24995
22 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE188364
ID:
200188364
18.

Long-Term Consumption Of Poultry Egg Products Provided Stable Growth Demographics, Body Composition, Glucose Control, And Liver Gene Expression In The Zebrafish Danio rerio

(Submitter supplied) Background: Poultry eggs are a low cost, high protein nutrient package that can be consumed as part of a quality diet. However, consumption of poultry egg products has been historically contentious, which highlights the importance of investigating impacts of long-term egg consumption on metabolic health. Objective: Our study utilized the zebrafish Danio rerio, a newly-defined model of human metabolic health, to understand the metabolic consequence of consuming egg products in lieu of other well-described protein sources. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
8 Samples
Download data: TAB
Series
Accession:
GSE184565
ID:
200184565
19.

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18413 GPL24995
82 Samples
Download data
Series
Accession:
GSE168362
ID:
200168362
20.

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ATAC-seq]

(Submitter supplied) Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18413
6 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE168361
ID:
200168361
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